Immune recognition

The immune response to viral infection comprises of the innate and adaptive responses. The adaptive response consists of cellular mediated response (T cell) and humoral (B cell or antibody-mediated) responses. Both responses are essential for antiviral defense and mediate immune memory response that is essential for rapid and efficient response to a subsequent encounter with a pathogen.

It is well established that neutralizing antibodies (nAbs) are key components in the protective immune responses to viral infections as they inhibit viral entry to host cells (for instance, by blocking the interactions with the host cell receptors or by preventing conformational changes required for viral entry). Consequently, nAbs can provide critical information on sites of vulnerability in the virus. Thus, a molecular-level understanding of viral neutralization by nAbs is imperative for the design of cross-protective vaccine antigens and the designing of cross-protective antiviral drugs.

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Virus-receptor interactions

Virus-host cell receptor interactions play a key regulatory role in the viral host range, tissue tropism, and viral pathogenesis. For envelope viruses, the binding of the virus to the host receptor can mediate conformational changes of the viral envelop proteins that trigger fusion of the virus membrane and cell membrane or endocytosis of the virus particle into the host cell. Understanding the envelope protein-receptor interactions can shade the light of the entry mechanism and viral tropism and advance the design of entry antivirals and prophylactic vaccines

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Viral entry mechanism 

Transferring genetic material across the membrane of host cells is an essential step for viral replication and pathogenesis. For enveloped viruses, this step is mediated by endocytosis and/or fusion of the viral envelope with the host cell membrane – an orchestrated process driven by the interactions of viral envelope glycoproteins (Env) with cofactors and receptors of the host cells to facilitate the virus entry. Recent biochemical and structural studies have shed light on the fusion and entry mechanism of numerous enveloped viruses (including HIV, influenza, Ebola, and Coronaviruses). To date, three structural classes of viral membrane fusion proteins have been identified, based on their mechanical and structural properties, termed class I, II, and III. However, structural studies of the Env glycoproteins from viruses that belong to the Pestivirus and Hepacivirus genus, e.g., the hepatitis C virus (HCV), have indicated that the fusion mechanism of these viruses is different from the known ones. Therefore, exploring and resolving the entry mechanism of these viruses will contribute to the discovery of novel fusion mechanisms and better control viral infection.

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HCV is a major global health burden. According to the last World Health Organization (WHO) global hepatitis report, approximately 0.8% of the world’s population was infected by HCV worldwide in 2019. HCV causes about 300,000 deaths and ~1.5 million new infections annually. Approximately 75% of HCV-infected people develop chronic infections that can lead to liver cirrhosis and, eventually, hepatocellular carcinoma. HCV is a major health concern in the Middle East, Central Asia, and Eastern Europe with a high estimated HCV prevalence (>3% of the population). In the US, HCV infection prevalence is approximately 1% with an unfortunate increase, since 2013, in the number of new infections. In Israel, the prevalence of HCV infection is approximately 1%.
Intense research over the past three decades has advanced our understanding of the HCV life-cycle and, inter alia, paved the way for the development of direct-acting antivirals (DAAs) that target non-structural proteins and effectively treat patients with persistent HCV infection. Nonetheless, DAA treatment faces several challenges e.g., late diagnostic, reinfections, DAA-resistant, and limited access to HCV diagnosis and treatment. Also, HCV infection induces an "epigenetic signature" following virus eradication by DAAs that cause the development of liver cancer. In parallel, the rise of a new HCV-infected generation, a direct consequence of the current opioid epidemic that unfortunately shows no signs of slowing down, intensifies the concern of HCV distribution and underscores the critical need for the development of an effective vaccine for HCV eradication.  
Diverse strategies for HCV vaccine development have been described; nevertheless, none has fully succeeded in eliciting a broad immune response, highlighting that alternative vaccination approaches are required to better control HCV spread. Understanding HCV immune recognition and entry mechanism can pave the way for the design of improved subunit vaccine immunogens to better combat HCV spread. 

Hepatitis C virus 

 

Bovine coronavirus (BCoV) is an RNA virus that causes respiratory and intestinal diseases in cattle and wild animals, resulting in economic losses to the beef and dairy industry. BCoV infection is associated with three significant clinical syndromes: (1) Winter dysentery (WD) characterized by hemorrhagic diarrhea in dairy cattle, causing a dramatic decrease in milk production and significant economic losses. (2) Calf diarrhea (CD) in dairy and beef calves in the first three weeks of life and characterized by severe diarrhea, sometimes bloody, and high mortality. (3) Respiratory infections in cattle of all ages, which can cause a decrease in milk production and high mortality (as part of the complex respiratory tract (BRDC)). 
Several commercial modified live or inactivated vaccines against BCoV are available. These vaccines contain, in most cases, one of two strains, the Mebus strain (the first strain isolated about fifty years ago) or strain C 1977. At present, it is not mandatory in Israel (as in the rest of the world) to vaccinate cattle against BCoV, but it is recommended to vaccinate pre-calving caws to provide protective immunity for the calves through the colostrum. Even though the vaccines have been commonly used for many years, most studies evaluating commercial vaccines report their safety and immunogenicity but do not report if they can elicit protective immunity. Some studies indicated that vaccines elicit only poor protective immunity against BRDC. In addition, field studies on the efficiency of the vaccines against WD and CD and if vaccination of pre-calving caws does elicit protective immunity for the calves are absent.
A recent field study, conducted by our collaborators at the Kimron Veterinary Institute, led by
Dr. Asaf Sol, in large dairy farms scattered in Israel indicated a genetic diversity among the strains currently circulating in Israel and between the local strains and the vaccines strain. These findings raise concerns about the effectiveness of vaccines currently used in Israel to elicit cross-genotype protective immunity.

Our research aims to investigate the adaptive humoral immunity and antibody neutralization response against BCoV. The working hypothesis is that a deep understanding of the antibody neutralization response against BCoV and high-resolution characterization of neutralization epitopes will serve as a platform for the structural-based design of an improved prophylactic vaccine to improve farm animals' welfare and minimize the farmer's economic damage.
 

Bovine CoV

Development of novel antimicrobial proteins

Antimicrobial-resistant bacterial pathogens constitute a significant risk to public health and caused approximately 1.25 million deaths in 2019. At the end of 2021, WHO has declared antimicrobial resistance as one of the top 10 global public health threats facing humanity. A significant concern is the rapid global spread of multi- and pan-resistant bacteria, which cause infections that cannot be treated with existing antimicrobial medicines. Unfortunately, the clinical antibiotics and antimicrobials pipeline runs dry, underscoring the significance of developing alternative approaches to treat bacterial infections.
For this purpose, our collaborators
@ the Levy lab have recently developed a precise algorithm that predicts new types of antimicrobial toxin proteins. Using the algorithm, they predicted and experimentally validated nine novel antimicrobial proteins that efficiently kill microbes like E. coli or S. cerevisiae yeast, demonstrating their potential to serve as a template for developing new antimicrobial drugs. Next, the Levy and the Tzarum labs aim to study the mechanism of selected antimicrobial proteins utilizing biochemical, biophysical, and structural tools. In parallel, we are studying the interactions of the discovered antimicrobial proteins with their immunity proteins that block the toxic phenotype. The newly discovered antimicrobial proteins will be used for the development of alternative antimicrobials to reduce the public health risk caused by resistant pathogenic bacteria and to discover novel antimicrobial mechanisms for future antibiotics.