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Article ; Online: Comparison of Subgenomic and Total RNA in SARS-CoV-2 Challenged Rhesus Macaques.

Dagotto, Gabriel / Mercado, Noe B / Martinez, David R / Hou, Yixuan J / Nkolola, Joseph P / Carnahan, Robert H / Crowe, James E / Baric, Ralph S / Barouch, Dan H

Journal of virology

2021 Volume 95, Issue 8

Abstract: Respiratory virus challenge studies involve administration of the challenge virus and sampling to assess for protection from the same anatomical locations. It can therefore be difficult to differentiate actively replicating virus from input challenge ... ...

Abstract	Respiratory virus challenge studies involve administration of the challenge virus and sampling to assess for protection from the same anatomical locations. It can therefore be difficult to differentiate actively replicating virus from input challenge virus. For SARS-CoV-2, specific monitoring of actively replicating virus is critical to investigate the protective and therapeutic efficacy of vaccines, monoclonal antibodies, and antiviral drugs. We developed a SARS-CoV-2 subgenomic RNA (sgRNA) RT-PCR assay to differentiate productive infection from inactivated or neutralized virus. Subgenomic RNAs are generated after cell entry and are poorly incorporate into mature virions, and thus may provide a marker for actively replicating virus. We show envelope (E) sgRNA was degraded by RNase in infected cell lysates, while genomic RNA (gRNA) was protected, presumably due to packaging into virions. To investigate the capacity of the sgRNA assay to distinguish input challenge virus from actively replicating virus
Language	English
Publishing date	2021-01-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.02370-20
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Article ; Online: Therapeutic efficacy of combined active and passive immunization in ART-suppressed, SHIV-infected rhesus macaques

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 8

Abstract: Antiretroviral therapy alone is insufficient in curing HIV-1 infection, due to latent viral reservoir persistency. Here, authors explore the post-virologic control of combining active and passive immunisation with vesatolimod, in a SHIV-infected rhesus ... ...

Abstract	Antiretroviral therapy alone is insufficient in curing HIV-1 infection, due to latent viral reservoir persistency. Here, authors explore the post-virologic control of combining active and passive immunisation with vesatolimod, in a SHIV-infected rhesus macaque model.
Keywords	Science ; Q
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Therapeutic efficacy of an Ad26/MVA vaccine with SIV gp140 protein and vesatolimod in ART-suppressed rhesus macaques.

NPJ vaccines

2022 Volume 7, Issue 1, Page(s) 53

Abstract: Developing an intervention that results in virologic control following discontinuation of antiretroviral therapy (ART) is a major objective of HIV-1 cure research. In this study, we investigated the therapeutic efficacy of a vaccine consisting of ... ...

Abstract	Developing an intervention that results in virologic control following discontinuation of antiretroviral therapy (ART) is a major objective of HIV-1 cure research. In this study, we investigated the therapeutic efficacy of a vaccine consisting of adenovirus serotype 26 (Ad26) and modified vaccinia Ankara (MVA) with or without an SIV Envelope (Env) gp140 protein with alum adjuvant in combination with the TLR7 agonist vesatolimod (GS-9620) in 36 ART-suppressed, SIVmac251-infected rhesus macaques. Ad26/MVA therapeutic vaccination led to robust humoral and cellular immune responses, and the Env protein boost increased antibody responses. Following discontinuation of ART, virologic control was observed in 5/12 animals in each vaccine group, compared with 0/12 animals in the sham control group. These data demonstrate therapeutic efficacy of Ad26/MVA vaccination with vesatolimod but no clear additional benefit of adding an Env protein boost. SIV-specific cellular immune responses correlated with virologic control. Our findings show partial efficacy of therapeutic vaccination following ART discontinuation in SIV-infected rhesus macaques.
Language	English
Publishing date	2022-05-18
Publishing country	England
Document type	Journal Article
ISSN	2059-0105
ISSN (online)	2059-0105
DOI	10.1038/s41541-022-00477-x
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Article ; Online: Therapeutic efficacy of combined active and passive immunization in ART-suppressed, SHIV-infected rhesus macaques.

Nature communications

2022 Volume 13, Issue 1, Page(s) 3463

Abstract: The latent viral reservoir is the critical barrier for developing an HIV-1 cure. Previous studies have shown that therapeutic vaccination or broadly neutralizing antibody (bNAb) administration, together with a Toll-like receptor 7 (TLR7) agonist, ... ...

Abstract	The latent viral reservoir is the critical barrier for developing an HIV-1 cure. Previous studies have shown that therapeutic vaccination or broadly neutralizing antibody (bNAb) administration, together with a Toll-like receptor 7 (TLR7) agonist, enhanced virologic control or delayed viral rebound, respectively, following discontinuation of antiretroviral therapy (ART) in SIV- or SHIV-infected rhesus macaques. Here we show that the combination of active and passive immunization with vesatolimod may lead to higher rates of post-ART virologic control compared to either approach alone. Therapeutic Ad26/MVA vaccination and PGT121 administration together with TLR7 stimulation with vesatolimod resulted in 70% post-ART virologic control in SHIV-SF162P3-infected rhesus macaques. These data suggest the potential of combining active and passive immunization targeting different immunologic mechanisms as an HIV-1 cure strategy.
MeSH term(s)	Animals ; HIV Infections/drug therapy ; HIV-1 ; Immunization, Passive ; Macaca mulatta ; Simian Acquired Immunodeficiency Syndrome ; Simian Immunodeficiency Virus ; Toll-Like Receptor 7 ; Viral Load
Chemical Substances	Toll-Like Receptor 7
Language	English
Publishing date	2022-06-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-31196-5
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Article ; Online: Defining the determinants of protection against SARS-CoV-2 infection and viral control in a dose-down Ad26.CoV2.S vaccine study in nonhuman primates.

Zhu, Daniel Y / Gorman, Matthew J / Yuan, Dansu / Yu, Jingyou / Mercado, Noe B / McMahan, Katherine / Borducchi, Erica N / Lifton, Michelle / Liu, Jinyan / Nampanya, Felix / Patel, Shivani / Peter, Lauren / Tostanoski, Lisa H / Pessaint, Laurent / Van Ry, Alex / Finneyfrock, Brad / Velasco, Jason / Teow, Elyse / Brown, Renita /

Cook, Anthony / Andersen, Hanne / Lewis, Mark G / Lauffenburger, Douglas A / Barouch, Dan H / Alter, Galit

PLoS biology

2022 Volume 20, Issue 5, Page(s) e3001609

Abstract: Despite the rapid creation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) vaccines, the precise correlates of immunity against severe Coronavirus Disease 2019 (COVID-19) are still unknown. Neutralizing antibodies represent a robust ... ...

Abstract	Despite the rapid creation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) vaccines, the precise correlates of immunity against severe Coronavirus Disease 2019 (COVID-19) are still unknown. Neutralizing antibodies represent a robust surrogate of protection in early Phase III studies, but vaccines provide protection prior to the evolution of neutralization, vaccines provide protection against variants that evade neutralization, and vaccines continue to provide protection against disease severity in the setting of waning neutralizing titers. Thus, in this study, using an Ad26.CoV2.S dose-down approach in nonhuman primates (NHPs), the role of neutralization, Fc effector function, and T-cell immunity were collectively probed against infection as well as against viral control. While dosing-down minimally impacted neutralizing and binding antibody titers, Fc receptor binding and functional antibody levels were induced in a highly dose-dependent manner. Neutralizing antibody and Fc receptor binding titers, but minimally T cells, were linked to the prevention of transmission. Conversely, Fc receptor binding/function and T cells were linked to antiviral control, with a minimal role for neutralization. These data point to dichotomous roles of neutralization and T-cell function in protection against transmission and disease severity and a continuous role for Fc effector function as a correlate of immunity key to halting and controlling SARS-CoV-2 and emerging variants.
MeSH term(s)	Ad26COVS1 ; Animals ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19/prevention & control ; COVID-19 Vaccines ; Humans ; Primates ; Receptors, Fc ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Chemical Substances	Ad26COVS1 (JT2NS6183B) ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines ; Receptors, Fc ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-05-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001609
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Article ; Online: Increased IL-6 expression precedes reliable viral detection in the rhesus macaque brain during acute SIV infection.

Gopalakrishnan, Raja Mohan / Aid, Malika / Mercado, Noe B / Davis, Caitlin / Malik, Shaily / Geiger, Emma / Varner, Valerie / Jones, Rhianna / Bosinger, Steven E / Piedra-Mora, Cesar / Martinot, Amanda J / Barouch, Dan H / Reeves, R Keith / Tan, C Sabrina

JCI insight

2021 Volume 6, Issue 20

Abstract: Knowledge of immune activation in the brain during acute HIV infection is crucial for the prevention and treatment of HIV-associated neurological disorders. We determined regional brain (basal ganglia, thalamus, and frontal cortex) immune and virological ...

Abstract	Knowledge of immune activation in the brain during acute HIV infection is crucial for the prevention and treatment of HIV-associated neurological disorders. We determined regional brain (basal ganglia, thalamus, and frontal cortex) immune and virological profiles at 7 and 14 days post infection (dpi) with SIVmac239 in rhesus macaques. The basal ganglia and thalamus had detectable viruses earlier (7 dpi) than the frontal cortex (14 dpi) and contained higher quantities of viruses than the latter. Increased immune activation of astrocytes and significant infiltration of macrophages in the thalamus at 14 dpi coincided with elevated plasma viral load, and SIV colocalized only within macrophages. RNA signatures of proinflammatory responses, including IL-6, were detected at 7 dpi in microglia and interestingly, preceded reliable detection of virus in tissues and were maintained in the chronically infected macaques. Countering the proinflammatory response, the antiinflammatory response was not detected until increased TGF-β expression was found in perivascular macrophages at 14 dpi. But this response was not detected in chronic infection. Our data provide evidence that the interplay of acute proinflammatory and antiinflammatory responses in the brain likely contributed to the overt neuroinflammation, where the immune activation preceded reliable viral detection.
MeSH term(s)	Acute Disease ; Animals ; Disease Models, Animal ; Interleukin-6/metabolism ; Macaca mulatta ; Simian Acquired Immunodeficiency Syndrome/genetics ; Simian Acquired Immunodeficiency Syndrome/pathology
Chemical Substances	Interleukin-6
Language	English
Publishing date	2021-10-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.152013
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Article ; Online: Reduced SARS-CoV-2 disease outcomes in Syrian hamsters receiving immune sera: Quantitative image analysis in pathologic assessments.

Veterinary pathology

2022 Volume 59, Issue 4, Page(s) 648–660

Abstract: There is a need to standardize pathologic endpoints in animal models of SARS-CoV-2 infection to help benchmark study quality, improve cross-institutional comparison of data, and assess therapeutic efficacy so that potential drugs and vaccines for SARS- ... ...

Abstract	There is a need to standardize pathologic endpoints in animal models of SARS-CoV-2 infection to help benchmark study quality, improve cross-institutional comparison of data, and assess therapeutic efficacy so that potential drugs and vaccines for SARS-CoV-2 can rapidly advance. The Syrian hamster model is a tractable small animal model for COVID-19 that models clinical disease in humans. Using the hamster model, the authors used traditional pathologic assessment with quantitative image analysis to assess disease outcomes in hamsters administered polyclonal immune sera from previously challenged rhesus macaques. The authors then used quantitative image analysis to assess pathologic endpoints across studies performed at different institutions using different tissue processing protocols. The authors detail pathological features of SARS-CoV-2 infection longitudinally and use immunohistochemistry to quantify myeloid cells and T lymphocyte infiltrates during SARS-CoV-2 infection. High-dose immune sera protected hamsters from weight loss and diminished viral replication in tissues and reduced lung lesions. Cumulative pathology scoring correlated with weight loss and was robust in distinguishing IgG efficacy. In formalin-infused lungs, quantitative measurement of percent area affected also correlated with weight loss but was less robust in non-formalin-infused lungs. Longitudinal immunohistochemical assessment of interstitial macrophage infiltrates showed that peak infiltration corresponded to weight loss, yet quantitative assessment of macrophage, neutrophil, and CD3+ T lymphocyte numbers did not distinguish IgG treatment effects. Here, the authors show that quantitative image analysis was a useful adjunct tool for assessing SARS-CoV-2 treatment outcomes in the hamster model.
MeSH term(s)	Animals ; COVID-19/veterinary ; COVID-19 Vaccines ; Cricetinae ; Disease Models, Animal ; Humans ; Immune Sera ; Immunoglobulin G ; Lung/pathology ; Macaca mulatta ; Mesocricetus ; SARS-CoV-2 ; Weight Loss
Chemical Substances	COVID-19 Vaccines ; Immune Sera ; Immunoglobulin G
Language	English
Publishing date	2022-05-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	188012-3
ISSN	1544-2217 ; 0300-9858
ISSN (online)	1544-2217
ISSN	0300-9858
DOI	10.1177/03009858221095794
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Article ; Online: Origin of rebound virus in chronically SIV-infected Rhesus monkeys following treatment discontinuation.

Liu, Po-Ting / Keele, Brandon F / Abbink, Peter / Mercado, Noe B / Liu, Jinyan / Bondzie, Esther A / Chandrashekar, Abishek / Borducchi, Erica N / Hesselgesser, Joseph / Mish, Michael / Chin, Gregory / Bekerman, Elena / Geleziunas, Romas / Barouch, Dan H

Nature communications

2020 Volume 11, Issue 1, Page(s) 5412

Abstract: Viral rebound following antiretroviral therapy (ART) discontinuation in HIV-1-infected individuals is believed to originate from a small pool of CD4+ T cells harboring replication-competent provirus. However, the origin and nature of the rebound virus ... ...

Abstract	Viral rebound following antiretroviral therapy (ART) discontinuation in HIV-1-infected individuals is believed to originate from a small pool of CD4+ T cells harboring replication-competent provirus. However, the origin and nature of the rebound virus has remained unclear. Recent studies have suggested that rebound virus does not originate directly from individual latent proviruses but rather from recombination events involving multiple proviruses. Here we evaluate the origin of rebound virus in 16 ART-suppressed, chronically SIV-infected rhesus monkeys following ART discontinuation. We sequence viral RNA and viral DNA in these animals prior to ART initiation, during ART suppression, and following viral rebound, and we compare rebound viral RNA after ART discontinuation with near full-length viral DNA from peripheral blood and lymph node mononuclear cells (PBMC and LNMC) during ART suppression. Sequences of initial rebound viruses closely match viral DNA sequences in PBMC and LNMC during ART suppression. Recombinant viruses are rare in the initial rebound virus populations but arise quickly within 2-4 weeks after viral rebound. These data suggest that intact proviral DNA in PBMC and LNMC during ART suppression is likely the direct origin of viral rebound in chronically SIV-infected rhesus monkeys following ART discontinuation.
MeSH term(s)	Animals ; Anti-Retroviral Agents/administration & dosage ; CD4-Positive T-Lymphocytes/virology ; Female ; HIV Infections/drug therapy ; HIV Infections/virology ; HIV-1/drug effects ; HIV-1/genetics ; HIV-1/physiology ; Humans ; Macaca mulatta ; Male ; Patient Dropouts ; Simian Acquired Immunodeficiency Syndrome/drug therapy ; Simian Acquired Immunodeficiency Syndrome/virology ; Simian Immunodeficiency Virus/drug effects ; Simian Immunodeficiency Virus/genetics ; Simian Immunodeficiency Virus/physiology ; Viral Load/drug effects ; Virus Latency/drug effects ; Virus Replication/drug effects
Chemical Substances	Anti-Retroviral Agents
Language	English
Publishing date	2020-10-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-19254-2
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Article ; Online: Feasibility and safety of ultrasound-guided minimally invasive autopsy in COVID-19 patients.

Brook, Olga R / Piper, Kimberly G / Mercado, Noe B / Gebre, Makda S / Barouch, Dan H / Busman-Sahay, Kathleen / Starke, Carly E / Estes, Jacob D / Martinot, Amanda J / Wrijil, Linda / Ducat, Sarah / Hecht, Jonathan L

Abdominal radiology (New York)

2020 Volume 46, Issue 3, Page(s) 1263–1271

Abstract: Objectives: To determine the feasibility and safety of ultrasound-guided minimally invasive autopsy in COVID-19 patients.: Methods: 60 patients who expired between 04/22/2020-05/06/2020 due to COVID-19 were considered for inclusion in the study, ... ...

Abstract	Objectives: To determine the feasibility and safety of ultrasound-guided minimally invasive autopsy in COVID-19 patients. Methods: 60 patients who expired between 04/22/2020-05/06/2020 due to COVID-19 were considered for inclusion in the study, based on availability of study staff. Minimally invasive ultrasound-guided autopsy was performed with 14G core biopsies through a 13G coaxial needle. The protocol required 20 cores of the liver, 30 of lung, 12 of spleen, 20 of heart, 20 of kidney, 4 of breast, 4 of testis, 2 of skeletal muscle, and 4 of fat with total of 112 cores per patient. Quality of the samples was evaluated by number, size, histology, immunohistochemistry, and in situ hybridization for COVID-19 and PCR-measured viral loads for SARS-CoV-2. Results: Five (5/60, 8%) patients were included. All approached families gave their consent for the minimally invasive autopsy. All organs for biopsy were successfully targeted with ultrasound guidance obtaining all required samples, apart from 2 patients where renal samples were not obtained due to atrophic kidneys. The number, size, and weight of the tissue cores met expectation of the research group and tissue histology quality was excellent. Pathology findings were concordant with previously reported autopsy findings for COVID-19. Highest SARS-CoV-2 viral load was detected in the lung, liver, and spleen that had small to moderate amount, and low viral load in was detected in the heart in 2/5 (40%). No virus was detected in the kidney (0/3, 0%). Conclusions: Ultrasound-guided percutaneous post-mortem core biopsies can safely provide adequate tissue. Highest SARS-CoV-2 viral load was seen in the lung, followed by liver and spleen with small amount in the myocardium.
MeSH term(s)	Aged ; Aged, 80 and over ; Autopsy/methods ; Biopsy ; COVID-19/pathology ; Feasibility Studies ; Female ; Humans ; Male ; Middle Aged ; SARS-CoV-2 ; Ultrasonography, Interventional/methods
Keywords	covid19
Language	English
Publishing date	2020-09-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2839786-1
ISSN	2366-0058 ; 2366-004X
ISSN (online)	2366-0058
ISSN	2366-004X
DOI	10.1007/s00261-020-02753-7
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Article ; Online: Long-acting capsid inhibitor protects macaques from repeat SHIV challenges.

Vidal, Samuel J / Bekerman, Elena / Hansen, Derek / Lu, Bing / Wang, Kelly / Mwangi, Judy / Rowe, William / Campigotto, Federico / Zheng, Jim / Kato, Darryl / Chandrashekar, Abishek / Barrett, Julia / Patel, Shivani / Wan, Huahua / Anioke, Tochi / Mercado, Noe B / Nkolola, Joseph P / Ferguson, Melissa J / Rinaldi, William J /

Callebaut, Christian / Blair, Wade / Cihlar, Tomas / Geleziunas, Romas / Yant, Stephen R / Barouch, Dan H

Nature

2021 Volume 601, Issue 7894, Page(s) 612–616

Abstract: Because no currently available vaccine can prevent HIV infection, pre-exposure prophylaxis (PrEP) with antiretrovirals (ARVs) is an important tool for combating the HIV ... ...

Abstract	Because no currently available vaccine can prevent HIV infection, pre-exposure prophylaxis (PrEP) with antiretrovirals (ARVs) is an important tool for combating the HIV pandemic
MeSH term(s)	Animals ; Anti-Retroviral Agents/pharmacology ; Capsid/drug effects ; Capsid Proteins/antagonists & inhibitors ; Capsid Proteins/metabolism ; Macaca mulatta ; Simian Acquired Immunodeficiency Syndrome/drug therapy ; Simian Acquired Immunodeficiency Syndrome/prevention & control ; Simian Acquired Immunodeficiency Syndrome/virology ; Simian Immunodeficiency Virus/drug effects
Chemical Substances	Anti-Retroviral Agents ; Capsid Proteins
Language	English
Publishing date	2021-12-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-021-04279-4
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