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Article: Necrotizing pneumonia due to

Hernández Solis, Alejandro / Rabadan Armenta, Saul Javier / Araiza Santibáñez, Javier / Bonifaz, Alexandro / Serna Valle, Fryda Jareth / Mojica Jaimes, Eliasib

Medical mycology case reports

2023 Volume 42, Page(s) 100603

Abstract: Saprochaete ... ...

Abstract	Saprochaete capitata
Language	English
Publishing date	2023-08-29
Publishing country	Netherlands
Document type	Case Reports
ZDB-ID	2670415-8
ISSN	2211-7539
ISSN	2211-7539
DOI	10.1016/j.mmcr.2023.08.006
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Article: Intrinsic furin-mediated cleavability of the spike S1/S2 site from SARS-CoV-2 variant B.1.1.529 (Omicron).

Lubinski, Bailey / Jaimes, Javier A / Whittaker, Gary R

bioRxiv : the preprint server for biology

2022

Abstract: The ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. SARS-CoV-2 The variant B.1.1.529 (Omicron) emerged in ... ...

Abstract	The ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. SARS-CoV-2 The variant B.1.1.529 (Omicron) emerged in late 2020 and has continued to evolve and is now present in several distinct sub-variants. Here, we analyzed the "furin cleavage site" of the spike protein of SARS-CoV-2 B.1.1.529 (Omicron variant)
Language	English
Publishing date	2022-07-26
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.04.20.488969
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Article: SARS-CoV-2 serosurvey of healthy, privately owned cats presenting to a New York City animal hospital in the early phase of the COVID-19 pandemic (2020-2021).

Choi, Annette / Stout, Alison E / Rollins, Alicia / Wang, Kally / Guo, Qinghua / Javier, A Jaimes / Kennedy, Monica / Wagner, Bettina / Whittaker, Gary R

bioRxiv : the preprint server for biology

2024

Abstract: Both domestic and non-domestic cats are now established to be susceptible to infection by SARS-CoV-2, the cause of the ongoing COVID-19 pandemic. While serious disease in cats may occur in some instances, the majority of infections appear to be ... ...

Abstract	Both domestic and non-domestic cats are now established to be susceptible to infection by SARS-CoV-2, the cause of the ongoing COVID-19 pandemic. While serious disease in cats may occur in some instances, the majority of infections appear to be subclinical. Differing prevalence data for SARS-CoV-2 infection of cats have been reported, and are highly context-dependent. Here, we report a retrospective serological survey of cats presented to an animal practice in New York City, located in close proximity to a large medical center that treated the first wave of COVID-19 patients in the US in the Spring of 2020. We sampled 79, mostly indoor, cats between June 2020 to May 2021, the early part of which time the community was under a strict public health "lock-down". Using a highly sensitive and specific fluorescent bead-based multiplex assay, we found an overall prevalence of 13/79 (16%) serologically-positive animals for the study period; however, cats sampled in the Fall of 2020 had a confirmed positive prevalence of 44%. For SARS-CoV-2 seropositive cats, we performed viral neutralization test with live SARS-CoV-2 to additionally confirm presence of SARS-CoV-2 specific antibodies. Of the thirteen seropositive cats, 7/13 (54%) were also positive by virus neutralization, and 2 of seropositive cats had previously documented respiratory signs, with high neutralization titers of 1:1024 and 1:4096; overall however, there was no statistically significant association of SARS-CoV-2 seropositivity with respiratory signs, or with breed, sex or age of the animals. Follow up sampling of cats, while limited in scope, showed that positive serological titers were maintained over time. In comparison, we found an overall confirmed positive prevalence of 51% for feline coronavirus (FCoV), an endemic virus of cats, with 30% confirmed negative for FCoV. We demonstrate the impact of SARS-CoV in a defined feline population during the first wave of SARS-CoV-2 infection of humans, and suggest that human-cat transmission was substantial in our study group. Our data provide a new context for SARS-CoV-2 transmission events across species.
Language	English
Publishing date	2024-02-15
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.13.580068
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Article ; Online: SARS-CoV-2 electrochemical immunosensor based on the spike-ACE2 complex.

Vásquez, Viviana / Navas, Maria-Cristina / Jaimes, Javier A / Orozco, Jahir

Analytica chimica acta

2022 Volume 1205, Page(s) 339718

Abstract: Rapid, straightforward, and massive diagnosis of coronavirus disease 2019 (COVID-19) is one of the more important measures to mitigate the current pandemics. This work reports on an immunosensor to rapidly detect the spike protein from the severe acute ... ...

Abstract	Rapid, straightforward, and massive diagnosis of coronavirus disease 2019 (COVID-19) is one of the more important measures to mitigate the current pandemics. This work reports on an immunosensor to rapidly detect the spike protein from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The immunosensing device entraps the spike protein linked to angiotensin-converting enzyme host receptor (ACE2) protein in a sandwich between carboxylated magnetic beads functionalized with an anti-spike antibody and an anti-ACE2 antibody, further labeled with streptavidin (poly)horseradish peroxidase (HRP) reporter enzyme. The particles were confined at the surface of screen-printed gold electrodes, whose signal resulting from the interaction of the enzyme with a mediator was recorded in a portable potentiostat. The immunosensor showed a sensitivity of 0.83 μA∗mL/μg and a limit of detection of 22.5 ng/mL of spike protein, with high reproducibility. As a proof-of-concept, it detected commercial spike protein-supplemented buffer solutions, pseudovirions, isolated viral particles and ten nasopharyngeal swab samples from infected patients compared to samples from three healthy individuals paving the way to detect the virus closer to the patient.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Biosensing Techniques/methods ; COVID-19/diagnosis ; Humans ; Immunoassay ; Protein Binding ; Reproducibility of Results ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-03-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1483436-4
ISSN	1873-4324 ; 0003-2670
ISSN (online)	1873-4324
ISSN	0003-2670
DOI	10.1016/j.aca.2022.339718
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Article ; Online: Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1/S2 site.

Jaimes, Javier A / Millet, Jean K / Whittaker, Gary R

SSRN

2020 , Page(s) 3581359

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19) has rapidly spread from an initial outbreak in Wuhan, China in December 2019 to the rest of the world within a few months. On March ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19) has rapidly spread from an initial outbreak in Wuhan, China in December 2019 to the rest of the world within a few months. On March 11
Keywords	covid19
Language	English
Publishing date	2020-05-05
Publishing country	United States
Document type	Preprint
ISSN	1556-5068
ISSN (online)	1556-5068
DOI	10.2139/ssrn.3581359
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Article ; Online: Intrinsic furin-mediated cleavability of the spike S1/S2 site from SARS-CoV-2 variant B.1.529 (Omicron)

Lubinski, Bailey / Jaimes, Javier A. / Whittaker, Gary

bioRxiv

Abstract: The ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. Here, we analyzed the S1/S2 cleavage site (also called ... ...

Abstract	The ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. Here, we analyzed the S1/S2 cleavage site (also called furin cleavage site) of the spike protein of SARS-CoV-2 B.1.529 (Omicron variant) in vitro, to assess the role of two key mutations (spike gene, N679K and P681H) compared to the ancestral B.1 virus. We observed significantly increased intrinsic cleavability with furin compared to an original B lineage virus (Wuhan-Hu-1) and two variants, B.1.1.7 (Alpha) and B.1.617 (Delta), that subsequently had wide circulation. Increased furin-mediated cleavage was attributed to the N679K mutation, which lies outside the conventional furin binding pocket. Our findings suggest that B.1.529 (Omicron variant) has gained genetic features linked to intrinsic furin cleavability, in line with its evolution within the population as the COVID-19 pandemic has proceeded.
Keywords	covid19
Language	English
Publishing date	2022-04-22
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.04.20.488969
Database	COVID19

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Article ; Online: Feline coronavirus: Insights into viral pathogenesis based on the spike protein structure and function.

Jaimes, Javier A / Whittaker, Gary R

Virology

2018 Volume 517, Page(s) 108–121

Abstract: Feline coronavirus (FCoV) is an etiological agent that causes a benign enteric illness and the fatal systemic disease feline infectious peritonitis (FIP). The FCoV spike (S) protein is considered the viral regulator for binding and entry to the cell. ... ...

Abstract	Feline coronavirus (FCoV) is an etiological agent that causes a benign enteric illness and the fatal systemic disease feline infectious peritonitis (FIP). The FCoV spike (S) protein is considered the viral regulator for binding and entry to the cell. This protein is also involved in FCoV tropism and virulence, as well as in the switch from enteric disease to FIP. This regulation is carried out by spike's major functions: receptor binding and virus-cell membrane fusion. In this review, we address important aspects in FCoV genetics, replication and pathogenesis, focusing on the role of S. To better understand this, FCoV S protein models were constructed, based on the human coronavirus NL63 (HCoV-NL63) S structure. We describe the specific structural characteristics of the FCoV S, in comparison with other coronavirus spikes. We also revise the biochemical events needed for FCoV S activation and its relation to the structural features of the protein.
MeSH term(s)	Animals ; Cats ; Coronavirus, Feline/genetics ; Coronavirus, Feline/metabolism ; Coronavirus, Feline/pathogenicity ; Feline Infectious Peritonitis/pathology ; Feline Infectious Peritonitis/virology ; Gene Expression Regulation, Viral/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Virus Replication
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, feline infectious peritonitis virus
Keywords	covid19
Language	English
Publishing date	2018-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2017.12.027
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Article ; Online: Proteolytic Cleavage of the SARS-CoV-2 Spike Protein and the Role of the Novel S1/S2 Site.

Jaimes, Javier A / Millet, Jean K / Whittaker, Gary R

iScience

2020 Volume 23, Issue 6, Page(s) 101212

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19) has rapidly spread to the entire world within a few months. The origin of SARS-CoV-2 has been related to the lineage B Betacoronavirus ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19) has rapidly spread to the entire world within a few months. The origin of SARS-CoV-2 has been related to the lineage B Betacoronavirus SARS-CoV and SARS-related coronaviruses found in bats. Early characterizations of the SARS-CoV-2 genome revealed the existence of a distinct four amino acid insert within the spike (S) protein (underlined, SPRRAR↓S), at the S1/S2 site located at the interface between the S1 receptor binding subunit and the S2 fusion subunit. Notably, this insert appears to be a distinguishing feature among SARS-related sequences and introduces a potential cleavage site for the protease furin. Here, we investigate the potential role of this novel S1/S2 cleavage site and present direct biochemical evidence for proteolytic processing by a variety of proteases. We discuss these findings in the context of the origin of SARS-CoV-2, viral stability, and transmission.
Keywords	covid19
Language	English
Publishing date	2020-05-28
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2020.101212
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Article ; Online: Molecular diversity of coronavirus host cell entry receptors.

Millet, Jean K / Jaimes, Javier A / Whittaker, Gary R

FEMS microbiology reviews

2020 Volume 45, Issue 3

Abstract: Coronaviruses are a group of viruses causing disease in a wide range of animals, and humans. Since 2002, the successive emergence of bat-borne severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS- ... ...

Abstract	Coronaviruses are a group of viruses causing disease in a wide range of animals, and humans. Since 2002, the successive emergence of bat-borne severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), swine acute diarrhea syndrome coronavirus (SADS-CoV) and SARS-CoV-2 has reinforced efforts in uncovering the molecular and evolutionary mechanisms governing coronavirus cell tropism and interspecies transmission. Decades of studies have led to the discovery of a broad set of carbohydrate and protein receptors for many animal and human coronaviruses. As the main determinant of coronavirus entry, the spike protein binds to these receptors and mediates membrane fusion. Prone to mutations and recombination, spike evolution has been studied extensively. The interactions between spike proteins and their receptors are often complex and despite many advances in the field, there remains many unresolved questions concerning coronavirus tropism modification and cross-species transmission, potentially leading to delays in outbreak responses. The emergence of SARS-CoV-2 underscores the need to address these outstanding issues in order to better anticipate new outbreaks. In this review, we discuss the latest advances in the field of coronavirus receptors emphasizing on the molecular and evolutionary processes that underlie coronavirus receptor usage and host range expansion.
MeSH term(s)	Animals ; Biodiversity ; COVID-19/metabolism ; COVID-19/virology ; Coronavirus/classification ; Coronavirus/physiology ; Coronavirus Infections/metabolism ; Coronavirus Infections/virology ; Genotype ; Host Specificity ; Host-Pathogen Interactions ; Humans ; Phylogeny ; Receptors, Coronavirus/chemistry ; Receptors, Coronavirus/classification ; Receptors, Coronavirus/metabolism ; SARS-CoV-2/classification ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Viral Tropism
Chemical Substances	Receptors, Coronavirus ; Spike Glycoprotein, Coronavirus
Keywords	covid19
Language	English
Publishing date	2020-10-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	283740-7
ISSN	1574-6976 ; 0168-6445
ISSN (online)	1574-6976
ISSN	0168-6445
DOI	10.1093/femsre/fuaa057
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Article ; Online: Knowledge, attitudes and experience of physicians working in Chile toward the prescription of pre-exposure prophylaxis (PrEP): A cross-national survey.

Orozco-Chinome, Javier E / Picón-Jaimes, Yelson A / Lozada-Martinez, Ivan D / Molina-Franky, Jessica / Bolaño Romero, Maria P / Acevedo-López, Doménica

International journal of STD & AIDS

2023 Volume 34, Issue 9, Page(s) 617–623

Abstract: Background: Pre-exposure prophylaxis (PrEP) involves administering antiretroviral drugs to prevent human immunodeficiency virus (HIV) infection in at-risk subjects. Chile is considered one of the countries with the highest number of new cases per year ... ...

Abstract	Background: Pre-exposure prophylaxis (PrEP) involves administering antiretroviral drugs to prevent human immunodeficiency virus (HIV) infection in at-risk subjects. Chile is considered one of the countries with the highest number of new cases per year of HIV infections. Methods: A nationwide cross-sectional study was carried out in Chile. A questionnaire of physicians' attitudes toward the prescription of PrEP was used. Results: 632 doctors responded correctly the survey. 58.5% ( Conclusion: It was concluded that knowledge, attitudes and experience toward PrEP prescribing are variable and related to patient care. However, Chile has a marked tendency in favor of this therapy, which is similar to that reported in studies worldwide.
MeSH term(s)	Humans ; Female ; Adult ; Male ; HIV Infections/drug therapy ; HIV Infections/prevention & control ; Pre-Exposure Prophylaxis/methods ; Cross-Sectional Studies ; Health Knowledge, Attitudes, Practice ; Chile ; Attitude of Health Personnel ; Anti-HIV Agents/therapeutic use ; Practice Patterns, Physicians' ; Physicians ; Surveys and Questionnaires ; Prescriptions ; Anti-Retroviral Agents/therapeutic use
Chemical Substances	Anti-HIV Agents ; Anti-Retroviral Agents
Language	English
Publishing date	2023-03-30
Publishing country	England
Document type	Journal Article
ZDB-ID	1018089-8
ISSN	1758-1052 ; 0956-4624
ISSN (online)	1758-1052
ISSN	0956-4624
DOI	10.1177/09564624231160576
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