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Article ; Online: Deletion of the SARS-CoV-2 Spike Cytoplasmic Tail Increases Infectivity in Pseudovirus Neutralization Assays.

Yu, Jingyou / Li, Zhenfeng / He, Xuan / Gebre, Makda S / Bondzie, Esther A / Wan, Huahua / Jacob-Dolan, Catherine / Martinez, David R / Nkolola, Joseph P / Baric, Ralph S / Barouch, Dan H

Journal of virology

2021 Volume 95, Issue 11

Abstract: Pseudotyped viruses are valuable tools for studying virulent or lethal viral pathogens that need to be handled in biosafety level 3 (BSL-3) or higher facilities. With the explosive spread of the coronavirus disease 2019 (COVID-19) pandemic, the ... ...

Abstract	Pseudotyped viruses are valuable tools for studying virulent or lethal viral pathogens that need to be handled in biosafety level 3 (BSL-3) or higher facilities. With the explosive spread of the coronavirus disease 2019 (COVID-19) pandemic, the establishment of a BSL-2 adapted SARS-CoV-2 pseudovirus neutralization assay is needed to facilitate the development of countermeasures. Here we describe an approach to generate a single-round lentiviral vector-based SARS-CoV-2 pseudovirus, which produced a signal more than 2 logs above background. Specifically, a SARS-CoV-2 spike variant with a cytoplasmic tail deletion of 13 amino acids, termed SΔCT13, conferred enhanced spike incorporation into pseudovirions and increased viral entry into cells as compared with full-length spike (S). We further compared S and SΔCT13 in terms of their sensitivity to vaccine sera, purified convalescent IgG, hACE2-mIgG, and the virus entry inhibitor BafA1. We developed a SΔCT13-based pseudovirus neutralization assay and defined key assay characteristics, including linearity, limit of detection, and intra- and intermediate-assay precision. Our data demonstrate that the SΔCT13-based pseudovirus shows enhanced infectivity in target cells, which will facilitate the assessment of humoral immunity to SARS-CoV-2 infection, antibody therapeutics, and vaccination. This pseudovirus neutralization assay can also be readily adapted to SARS-CoV-2 variants that emerge.
Language	English
Publishing date	2021-03-16
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.00044-21
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Article ; Online: Durability and expansion of neutralizing antibody breadth following Ad26.COV2.S vaccination of mice.

Mahrokhian, Shant H / Tostanoski, Lisa H / Jacob-Dolan, Catherine / Zahn, Roland C / Wegmann, Frank / McMahan, Katherine / Yu, Jingyou / Gebre, Makda S / Bondzie, Esther A / Wan, Huahua / Powers, Olivia / Ye, Tianyi / Barrett, Julia / Schuitemaker, Hanneke / Barouch, Dan H

NPJ vaccines

2022 Volume 7, Issue 1, Page(s) 23

Abstract: Emerging SARS-CoV-2 variants with the potential to escape binding and neutralizing antibody responses pose a threat to vaccine efficacy. We recently reported expansion of broadly neutralizing activity of vaccine-elicited antibodies in humans 8 months ... ...

Abstract	Emerging SARS-CoV-2 variants with the potential to escape binding and neutralizing antibody responses pose a threat to vaccine efficacy. We recently reported expansion of broadly neutralizing activity of vaccine-elicited antibodies in humans 8 months following a single immunization with Ad26.COV2.S. Here, we assessed the 15-month durability of antibody responses and their neutralizing capacity to B.1.617.2 (delta) and B.1.351 (beta) variants following a single immunization of Ad26.COV2.S in mice. We report the persistence of binding and neutralizing antibody titers following immunization with a concomitant increase in neutralizing antibody breadth to delta and beta variants over time. Evaluation of bone marrow and spleen at 15 months postimmunization revealed that Ad26.COV2.S-immunized mice tissues contained spike-specific antibody-secreting cells. We conclude that immunization with Ad26.COV2.S elicits a robust immune response against SARS-CoV-2 spike, which expands over time to neutralize delta and beta variants more robustly, and seeds bone marrow and spleen with long-lived spike-specific antibody-secreting cells. These data extend previous findings in humans and support the use of a mouse model as a potential tool to further explore the dynamics of the humoral immune response following vaccination with Ad26.COV2.S.
Language	English
Publishing date	2022-02-23
Publishing country	England
Document type	Journal Article
ISSN	2059-0105
ISSN (online)	2059-0105
DOI	10.1038/s41541-022-00454-4
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Article: Comparable Neutralization of the SARS-CoV-2 Omicron BA.1 and BA.2 Variants.

Yu, Jingyou / Collier, Ai-Ris Y / Rowe, Marjorie / Mardas, Fatima / Ventura, John D / Wan, Huahua / Miller, Jessica / Powers, Olivia / Chung, Benjamin / Siamatu, Mazuba / Hachmann, Nicole P / Surve, Nehalee / Nampanya, Felix / Chandrashekar, Abishek / Barouch, Dan H

medRxiv : the preprint server for health sciences

2022

Abstract: The SARS-CoV-2 Omicron variant (B.1.1.529) has three major lineages BA.1, BA.2, and BA ... ...

Abstract	The SARS-CoV-2 Omicron variant (B.1.1.529) has three major lineages BA.1, BA.2, and BA.3
Language	English
Publishing date	2022-02-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.02.06.22270533
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Article ; Online: A bivalent SARS-CoV-2 monoclonal antibody combination does not affect the immunogenicity of a vector-based COVID-19 vaccine in macaques.

Nkolola, Joseph P / Yu, Jingyou / Wan, Huahua / Chang, Aiquan / McMahan, Katherine / Anioke, Tochi / Jacob-Dolan, Catherine / Powers, Olivia / Ye, Tianyi / Chandrashekar, Abishek / Sellers, Daniel / Barrett, Julia / Loo, Yueh-Ming / Esser, Mark T / Carnahan, Robert H / Crowe, James E / Barouch, Dan H

Science translational medicine

2022 Volume 14, Issue 665, Page(s) eabo6160

Abstract: Human monoclonal antibodies (mAbs) that target the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) offer a promising approach for the prevention and treatment of coronavirus disease 2019 (COVID-19). Given suboptimal ... ...

Abstract	Human monoclonal antibodies (mAbs) that target the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) offer a promising approach for the prevention and treatment of coronavirus disease 2019 (COVID-19). Given suboptimal global vaccination rates, waning immunity in vaccinated individuals, and the emergence of SARS-CoV-2 variants of concern, the use of mAbs for COVID-19 prevention may increase and may need to be administered together with vaccines in certain settings. However, it is unknown whether administration of mAbs will affect the immunogenicity of SARS-CoV-2 vaccines. Using an adenovirus vector-based SARS-CoV-2 vaccine, we show that simultaneous administration of the vaccine with SARS-CoV-2 mAbs does not diminish vaccine-induced humoral or cellular immunity in cynomolgus macaques. These results suggest that SARS-CoV-2 mAbs and viral vector-based SARS-CoV-2 vaccines can be administered together without loss of potency of either product. Additional studies will be required to evaluate coadministration of mAbs with other vaccine platforms.
MeSH term(s)	Animals ; Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19/prevention & control ; COVID-19 Vaccines ; Humans ; Macaca ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Vaccination ; Viral Vaccines
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus ; Viral Vaccines ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.abo6160
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Article ; Online: Neutralization of the SARS-CoV-2 Omicron BA.1 and BA.2 Variants.

The New England journal of medicine

2022 Volume 386, Issue 16, Page(s) 1579–1580

MeSH term(s)	Antibodies, Neutralizing/immunology ; Antibodies, Neutralizing/therapeutic use ; COVID-19/immunology ; COVID-19/prevention & control ; COVID-19/therapy ; Humans ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus
Chemical Substances	Antibodies, Neutralizing ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-03-16
Publishing country	United States
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc2201849
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Article ; Online: rRNA adenine methylation requires T07A9.8 gene as rram-1 in Caenorhabditis elegans.

Yokoyama, Wataru / Hirota, Keiko / Wan, Huahua / Sumi, Naoaki / Miyata, Mai / Araoi, Sho / Nomura, Naoto / Kako, Koichiro / Fukamizu, Akiyoshi

Journal of biochemistry

2018 Volume 163, Issue 6, Page(s) 465–474

Abstract: RNAs are post-transcriptionally modified in all kingdoms of life. Of these modifications, base methylations are highly conserved in eukaryote ribosomal RNA (rRNA). Recently, rRNA processing protein 8 (Rrp8) and nucleomethylin (NML) were identified as ... ...

Abstract	RNAs are post-transcriptionally modified in all kingdoms of life. Of these modifications, base methylations are highly conserved in eukaryote ribosomal RNA (rRNA). Recently, rRNA processing protein 8 (Rrp8) and nucleomethylin (NML) were identified as factors of N1-methyladenosine (m1A) modification in yeast 25 S and mammalian 28 S rRNA, respectively. However, m1A modification of rRNA is still poorly understood in Caenorhabditis elegans (C. elegans). Here, using the liquid chromatography/tandem mass spectrometry analysis and RNA immunoprecipitation assay, we have identified that the m1A modification is located around position 674 (A674) of 26 S rRNA in C. elegans. Furthermore, quantitative PCR-based analysis revealed that T07A9.8, a C. elegans homolog of yeast Rrp8 and human NML, is responsible for m1A modification at A674 of 26 S rRNA. This m1A modification site in C. elegans corresponds to those in yeast 25 S rRNA and human 28 S rRNA. Intriguingly, T07A9.8 is not associated with pre-rRNA transcription under normal nutrient conditions. Since the m1A modification of 26 S rRNA requires T07A9.8 in C. elegans, we designated the gene as rRNA adenine methyltransferase-1 (rram-1).
MeSH term(s)	Adenine/metabolism ; Animals ; Caenorhabditis elegans/enzymology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Methylation ; RNA, Ribosomal/chemistry ; RNA, Ribosomal/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/genetics ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/metabolism
Chemical Substances	RNA, Ribosomal ; Site-Specific DNA-Methyltransferase (Adenine-Specific) (EC 2.1.1.72) ; Adenine (JAC85A2161)
Language	English
Publishing date	2018-06-01
Publishing country	England
Document type	Journal Article
ZDB-ID	218073-x
ISSN	1756-2651 ; 0021-924X
ISSN (online)	1756-2651
ISSN	0021-924X
DOI	10.1093/jb/mvy018
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Uc I Zs.202: Show issues

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Article ; Online: Correlates of Neutralization against SARS-CoV-2 Variants of Concern by Early Pandemic Sera.

Vidal, Samuel J / Collier, Ai-Ris Y / Yu, Jingyou / McMahan, Katherine / Tostanoski, Lisa H / Ventura, John D / Aid, Malika / Peter, Lauren / Jacob-Dolan, Catherine / Anioke, Tochi / Chang, Aiquan / Wan, Huahua / Aguayo, Ricardo / Ngo, Debby / Gerszten, Robert E / Seaman, Michael S / Barouch, Dan H

Journal of virology

2021 Volume 95, Issue 14, Page(s) e0040421

Abstract: Emerging SARS-CoV-2 variants of concern that overcome natural and vaccine-induced immunity threaten to exacerbate the COVID-19 pandemic. Increasing evidence suggests that neutralizing antibody (NAb) responses are a primary mechanism of protection against ...

Abstract	Emerging SARS-CoV-2 variants of concern that overcome natural and vaccine-induced immunity threaten to exacerbate the COVID-19 pandemic. Increasing evidence suggests that neutralizing antibody (NAb) responses are a primary mechanism of protection against infection. However, little is known about the extent and mechanisms by which natural immunity acquired during the early COVID-19 pandemic confers cross-neutralization of emerging variants. In this study, we investigated cross-neutralization of the B.1.1.7 and B.1.351 SARS-CoV-2 variants in a well-characterized cohort of early pandemic convalescent subjects. We observed modestly decreased cross-neutralization of B.1.1.7 but a substantial 4.8-fold reduction in cross-neutralization of B.1.351. Correlates of cross-neutralization included receptor binding domain (RBD) and N-terminal domain (NTD) binding antibodies, homologous NAb titers, and membrane-directed T cell responses. These data shed light on the cross-neutralization of emerging variants by early pandemic convalescent immune responses.
MeSH term(s)	Adult ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; COVID-19/epidemiology ; COVID-19/immunology ; Cross Reactions ; Humans ; Male ; Pandemics ; SARS-CoV-2/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral
Language	English
Publishing date	2021-06-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00404-21
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Zs.A 609: Show issues

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Article ; Online: Protective Efficacy of Rhesus Adenovirus COVID-19 Vaccines against Mouse-Adapted SARS-CoV-2.

Tostanoski, Lisa H / Gralinski, Lisa E / Martinez, David R / Schaefer, Alexandra / Mahrokhian, Shant H / Li, Zhenfeng / Nampanya, Felix / Wan, Huahua / Yu, Jingyou / Chang, Aiquan / Liu, Jinyan / McMahan, Katherine / Ventura, John D / Dinnon, Kenneth H / Leist, Sarah R / Baric, Ralph S / Barouch, Dan H

Journal of virology

2021 Volume 95, Issue 23, Page(s) e0097421

Abstract: The global COVID-19 pandemic has sparked intense interest in the rapid development of vaccines as well as animal models to evaluate vaccine candidates and to define immune correlates of protection. We recently reported a mouse-adapted SARS-CoV-2 virus ... ...

Abstract	The global COVID-19 pandemic has sparked intense interest in the rapid development of vaccines as well as animal models to evaluate vaccine candidates and to define immune correlates of protection. We recently reported a mouse-adapted SARS-CoV-2 virus strain (MA10) with the potential to infect wild-type laboratory mice, driving high levels of viral replication in respiratory tract tissues as well as severe clinical and respiratory symptoms, aspects of COVID-19 disease in humans that are important to capture in model systems. We evaluated the immunogenicity and protective efficacy of novel rhesus adenovirus serotype 52 (RhAd52) vaccines against MA10 challenge in mice. Baseline seroprevalence is lower for rhesus adenovirus vectors than for human or chimpanzee adenovirus vectors, making these vectors attractive candidates for vaccine development. We observed that RhAd52 vaccines elicited robust binding and neutralizing antibody titers, which inversely correlated with viral replication after challenge. These data support the development of RhAd52 vaccines and the use of the MA10 challenge virus to screen novel vaccine candidates and to study the immunologic mechanisms that underscore protection from SARS-CoV-2 challenge in wild-type mice.
MeSH term(s)	Adenoviridae Infections/immunology ; Adenovirus Vaccines/immunology ; Adenoviruses, Simian/immunology ; Animals ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; COVID-19/immunology ; COVID-19/prevention & control ; COVID-19 Vaccines/immunology ; Disease Models, Animal ; Female ; Humans ; Immunogenicity, Vaccine ; Macaca mulatta/virology ; Mice ; Mice, Inbred BALB C ; Pandemics/prevention & control ; SARS-CoV-2/immunology ; SARS-CoV-2/pathogenicity ; Vaccination
Chemical Substances	Adenovirus Vaccines ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines
Language	English
Publishing date	2021-09-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00974-21
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Zs.A 609: Show issues

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Article: Protective efficacy of rhesus adenovirus COVID-19 vaccines against mouse-adapted SARS-CoV-2.

Tostanoski, Lisa H / Gralinski, Lisa E / Martinez, David R / Schaefer, Alexandra / Mahrokhian, Shant H / Li, Zhenfeng / Nampanya, Felix / Wan, Huahua / Yu, Jingyou / Chang, Aiquan / Liu, Jinyan / McMahan, Katherine / Dinnon, Kenneth H / Leist, Sarah R / Baric, Ralph S / Barouch, Dan H

bioRxiv : the preprint server for biology

2021

Abstract	The global COVID-19 pandemic has sparked intense interest in the rapid development of vaccines as well as animal models to evaluate vaccine candidates and to define immune correlates of protection. We recently reported a mouse-adapted SARS-CoV-2 virus strain (MA10) with the potential to infect wild-type laboratory mice, driving high levels of viral replication in respiratory tract tissues as well as severe clinical and respiratory symptoms, aspects of COVID-19 disease in humans that are important to capture in model systems. We evaluated the immunogenicity and protective efficacy of novel rhesus adenovirus serotype 52 (RhAd52) vaccines against MA10 challenge in mice. Baseline seroprevalence is lower for rhesus adenovirus vectors than for human or chimpanzee adenovirus vectors, making these vectors attractive candidates for vaccine development. We observed that RhAd52 vaccines elicited robust binding and neutralizing antibody titers, which inversely correlated with viral replication after challenge. These data support the development of RhAd52 vaccines and the use of the MA10 challenge virus to screen novel vaccine candidates and to study the immunologic mechanisms that underscore protection from SARS-CoV-2 challenge in wild-type mice. Importance: We have developed a series of SARS-CoV-2 vaccines using rhesus adenovirus serotype 52 (RhAd52) vectors, which exhibits a lower seroprevalence than human and chimpanzee vectors, supporting their development as novel vaccine vectors or as an alternative Ad vector for boosting. We sought to test these vaccines using a recently reported mouse-adapted SARS-CoV-2 (MA10) virus to i) evaluate the protective efficacy of RhAd52 vaccines and ii) further characterize this mouse-adapted challenge model and probe immune correlates of protection. We demonstrate RhAd52 vaccines elicit robust SARS-CoV-2-specific antibody responses and protect against clinical disease and viral replication in the lungs. Further, binding and neutralizing antibody titers correlated with protective efficacy. These data validate the MA10 mouse model as a useful tool to screen and study novel vaccine candidates, as well as the development of RhAd52 vaccines for COVID-19.
Language	English
Publishing date	2021-06-15
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.06.14.448461
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Article ; Online: mRNA booster vaccination protects aged mice against the SARS-CoV-2 Omicron variant.

Communications biology

2022 Volume 5, Issue 1, Page(s) 790

Abstract: The SARS-CoV-2 Omicron variant evades vaccine-induced immunity. While a booster dose of ancestral mRNA vaccines effectively elicits neutralizing antibodies against variants, its efficacy against Omicron in older adults, who are at the greatest risk of ... ...

Abstract	The SARS-CoV-2 Omicron variant evades vaccine-induced immunity. While a booster dose of ancestral mRNA vaccines effectively elicits neutralizing antibodies against variants, its efficacy against Omicron in older adults, who are at the greatest risk of severe disease, is not fully elucidated. Here, we evaluate multiple longitudinal immunization regimens of mRNA BNT162b2 to assess the effects of a booster dose provided >8 months after the primary immunization series across the murine lifespan, including in aged 21-month-old mice. Boosting dramatically enhances humoral and cell-mediated responses with evidence of Omicron cross-recognition. Furthermore, while younger mice are protected without a booster dose, boosting provides sterilizing immunity against Omicron-induced lung infection in aged 21-month-old mice. Correlational analyses reveal that neutralizing activity against Omicron is strongly associated with protection. Overall, our findings indicate age-dependent vaccine efficacy and demonstrate the potential benefit of mRNA booster immunization to protect vulnerable older populations against SARS-CoV-2 variants.
MeSH term(s)	Animals ; Antibodies, Viral ; BNT162 Vaccine ; COVID-19/prevention & control ; Humans ; Mice ; Mice, Inbred BALB C ; RNA, Messenger/genetics ; SARS-CoV-2 ; Vaccination ; Viral Vaccines/genetics
Chemical Substances	Antibodies, Viral ; RNA, Messenger ; Viral Vaccines ; BNT162 Vaccine (N38TVC63NU)
Language	English
Publishing date	2022-08-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-03765-3
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