Model of coronavirus dual entry pathway. This model depicts the two methods of viral entry: early pathway and late pathway. As the virus binds to its receptor (1), it can achieve entry via two routes: plasma membrane or endosome. For SARS-CoV: The presence of exogeneous and membrane bound proteases, such as trypsin and TMPRSS2, triggers the early fusion pathway (2a). Otherwise, it will be endocytosed (2b, 3). For MERS-CoV: If furin cleaved the S protein at S1/S2 during biosynthesis, exogeneous and membrane bound proteases, such as trypsin and TMPRSS2, will trigger early entry (2a). Otherwise, it will be cleaved at the S1/S2 site (2b) causing the virus to be endocytosed (3). For both: Within the endosome, the low pH activates cathepsin L (4), cleaving S2′ site, triggering the fusion pathway and releasing the CoV genome. Upon viral entry, copies of the genome are made in the cytoplasm (5), where components of the spike protein are synthesized in the rough endoplasmic reticulum (ER) (6). The structural proteins are assembled in the ER-Golgi intermediate compartment (ERGIC), where the spike protein can be pre-cleaved by furin, depending on cell type (7), followed by release of the virus from the cell (8, 9). For SARS-CoV-2: Studies currently show that SARS-CoV-2 can utilize membrane bound TMPRSS2 or endosomal cathepsin L for entry and that the S protein is processed during biosynthesis. Other factors that can influence the viral entry pathway are calcium and cholesterol (not shown).
Early studies in virology
I have studied viruses for several years. I started my career in virology early in my undergraduate education, when I joined Dr. Victor Vera and Dr. Gloria Ramirez's lab at University Nacional de Colombia. There I studied the pathogenesis of the avian coronavirus (CoV) bronchitis virus (IBV). Specifically, I wanted to uncover the pathological characteristics of a recently isolated strain of the virus, which was genetically similar to a group of IBV strains that were later known as QX strains, which caused a more aggressive disease in domestic birds. This work allowed me to take my first steps in research and also awoke in continuing investigating about viruses.
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As a continuation of my work, I stayed in this lab to pursue a master's degree. During this time, my research focused on molecular diagnostics and the evaluation of vaccine efficacy against another avian virus, the infectious burial disease virus (IBDV). In my research, I observed how a newly introduced IBDV vaccine failed to induce a protective immune response in the animals, and on the contrary, caused strong adverse effects in their immune system.
A and B: Normal lymphocytes in the bursa. C and D: Lymphocyte depletion caused by the studied vaccine. Foto credits: Javier A. Jaimes
Past and ongoing coronavirus research
Figure A: FIPV I Black S protein model and cleavage sites. S1/S2 cleavage site is protruding from the protein forming a 19 amino acid loop (dotted line circle). Location and magnification of FIPV I Black S1/S2 cleavage site (bright green) and flanking amino acids (orange): Thr 783 and Pro 802. Location and magnification of FIPV I Black S2’ cleavage site (yellow). Figure and legend source: Jaimes JA, Whittaker GR. Virology. 2018 Apr;517:108-121. doi: 10.1016/j.virol.2017.12.027
For 8 years, I studded the pathogenesis of human and animal coronaviruses (CoVs). I especially focused on the mechanisms used by these CoVs to entry into the host cell. My PhD research aimed to uncover the bimolecular cell entry pathways of the feline coronavirus (FCoV). This virus is known to cause a mild to moderate disease in most of the infected felids (domestic and wild). However, some of these animals could develop the nasty and almost always deadly (in untreated) feline infectious peritonitis (FIP), a pathology that resulted from a viral internal mutation. In my research, I focused on the mechanistic features of the FCoV spike protein, which is the viral regulator for cell entry. I studied the structure of this protein in silico and observed a functional structural loop that is suggested to be key in the transition to FIP. I also studied how changes in the amino acid sequence of this loop, introducing changes in the proteolytic requirements for activation, resulting in an altered entry pathway.
In December 2019, a new CoV emerged from wild animal reservoirs to cause the coronavirus disease 2019 (COVID-19), which rapidly became a pandemic in early 2020. The virus, known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the focus of the interest of many researchers around the globe, due to its high rate of transmission and the ability to constantly evolve into new genetic variants. Since the very early days of the SARS-CoV-2 emergency, I have worked on the study of this virus and its mechanisms of infection of susceptible cells. My research has focused on understanding of the structural and biochemical characteristics of the viral spike protein. Under the advising of Professor Gary Whittaker at Cornell University, I published several research articles addressing the function of this protein and the implications in viral entry. We characterized the proteolytic requirements for several SARS-CoV-2 variants in an attempt to understand the evolutionary consequences of mutations at the protein's activation site. In collaboration with Dr. Julian Ruiz-Saenz from Universidad Cooperativa de Colombia, we have also studied the susceptibility of domestic and wild species to SARS-CoV-2 and their potential role in the transmission of the virus. I also participated in two studies in collaboration with the Daniel and Cantley research groups at Cornel University and Weill Cornell Medicine (respectively), to explore alternative mechanisms used by the SARS-CoV-2 spike to force viral-cell membrane fusion, as well as the potential targeting of these mechanisms for therapeutics.
Panel left: SARS-CoV-2 spike protein structural homology model. This model was predicted during the early days in the COVID-19 pandemic when the cry-EM structure was unavailable. Our model predicted a flexible loop at the S1/S2 boundary, which is functionally key for viral entry. Figure source: Jaimes JA, André NM, Chappie JS, Millet JK, Whittaker GR. J Mol Biol. 2020 May 1;432(10):3309-3325. doi: 10.1016/j.jmb.2020.04.009. Panel right: TMPRSS2 expressing Vero E6 cells and expressing the SARS-CoV-2 spike protein from the wild type (WT), the B.1.1.7 variant (Alpha) and the WT harboring the P681H mutation. We observed no difference in syncytia (cell-cell fusion) formation. S- means no spike is expressed. Figure source: Lubinski B, Fernandes MHV, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. iScience. 2022 Jan 21;25(1):103589. doi: 10.1016/j.isci.2021.103589.
I recently joined Jeremy Luban’s laboratory at the University of Massachusetts Chan Medical School where I continued investigating the SARS-CoV-2 pathogenesis. In the Luban lab, I have mainly focused on the studying gateway mutations that may have increased the viral fitness and facilitated the emergence of SARS-CoV-2 variants during the course of the epidemic. Early after the explosion of COVID-19 cases, our lab reported the occurrence of the D614G mutation, that is believed to precede the emerging lineage B variants that appeared through the last 3 years. In a recent study, we addressed the role of other mutations (i.e.: H655Y and Q613H) and their potential to also act as a gateway for other variants. We also have studied their role in the structure and the mechanisms of infection in the SARS-CoV-2. This is an ongoing project, and we keep exploring other mutations with similar potential.
Panel left: A graphical illustration on the importance of the D614G and the H655Y mutations in the stability of the spike protein in SARS-CoV-2 variants. Panels G, I and K: Impact of the D614G and the H655Y mutations in the infectivity of pseudovirus decorated with the Wuhan-Hu-1, Gamma and Omicron (BA.1) spike proteins. Figures source: Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. bioRxiv. 2023 Apr 24:2023.03.30.535005. doi: 10.1101/2023.03.30.535005. Preprint.
We have also collaborated with the Marks, Seaman, and Lemieux labs at Harvard University, to develop tools to predict the impact of spike mutations in future emerging variants. In this project, the participating labs have contributed to design a mathematical model that predicts the impact of mutations in the infectivity of the virus, as well as in its ability to avoid the immune response induced by vaccines and/or previous infections. This is a very exciting project, with potential to impact the way on how vaccines are developed.
Ebola virus and other ongoing projects
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During the past year, I have expanded the focus of my research to other emergent viruses (i.e.: Ebola virus – EBOV). EBOV cause a dramatic hemorrhagic disease with a fatality rate that can be >90%, depending on the viral strain. In the past years we have witnessed several EBOV outbreaks in west Africa, that have caught the attention of the scientific community (as well as the general public), due to the severity of the caused disease and the devastating potential of these viruses if they spread and cause a major epidemic. During two major outbreaks (Makona region in 2013 and Kivu region in 2016), some mutations in the EBOV glycoprotein (GP) have been suggested to have a gateway potential to increase the fitness of the virus, facilitating its spread and evolution. I am currently studying the role of those mutations on the infectivity and the structural stability of the EBOV GP. This project has become my main interest, due the implications of this virus, and also because of the similarities on the behavior of these mutations, to the ones occurring in SARS-CoV-2.
Future research interests
The emergency of several viral agents of disease have shown us the risks these microorganisms pose and the potential consequences for the public health. CoVs are well known for constantly emerge from wild reservoirs to cause disease in both humans and animals. However, these are not the only viruses that pose a threat for emergency. Bunyaviruses, are yet another group of viruses with potential to cause massive epidemics, specially (but not exclusively) in tropical regions. For my future research endeavors, I aim to study these viruses and their implications for the infected cell. I will use my previous and current experience studying the pathogenesis of CoVs, to investigate the mechanisms of entry into the host cell of emerging and potentially emerging bunyaviruses. My goal is to contribute as much as I can to the understanding of these viruses, so in the event of an epidemic, we can be more prepared to respond to this threat.