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Research Overview

Our long-term research objectives are to understand, in mechanistic detail, how RNA viruses enter, replicate, express genetic information, and bud from cells, to understand viral pathogenesis, and to facilitate the rational design and development of new vaccines and anti-viral drugs. Our general strategy is to focus on human metapneumovirus and avian metapneumovirus (members of Paramyxoviridae, non-segmented negative-sense RNA viruses) and human norovirus (a member of Caliciviridae, positive-sense RNA virus).

Research interest I: Human metapneumovirus (hMPV) and avian metapneumovirus (aMPV).

The family Paramyxoviridae includes two subfamilies: Pneumovirinae and Paramyxovirinae. The subfamily Pneumovirinae includes a number of significant human and animal respiratory pathogens such as human respiratory syncytial virus (hRSV), bovine RSV (bRSV), human metapneumovirus (hMPV), avian metapneumovirus (aMPV), and pneumonia virus ofmice (PVM). Examples of Paramyxovirinae include human parainfluenza virus type 3 (PIV3), measles, mumps, and Hendra and Nipah viruses.  Among the paramyxoviruses, hMPV, RSV, and PIV3 account for more than 70% of acute viral respiratory diseases, most notably  in infants, children, and the elderly. Together these viruses are responsible for the majority of respiratory tract diseases and inflict significant economic and emotional burdens. For many of these viruses, there are no effective vaccines or anti-viral drugs.

Project 1: Understand the mechanism of metapneumovirus entry. 

Paramyxoviruses enter host cells by fusing the viral envelope with a host cell membrane. This is mediated by membrane fusion induced by surface glycoprotein spikes. For viruses in the Paramyxovirinae subfamily, it is firmly established that membrane fusion requires a specific interaction between two glycoproteins, the attachment protein and the fusion (F) protein, with fusion occurring at neutral pH. However, membrane fusion of pneumoviruses appears to be unique, in that fusion is accomplished by the F protein alone without help from the attachment glycoprotein. In addition, some hMPV strains require low pH for fusion to occur. Our lab has chosen to study two closely related pneumoviruses, hMPV and aMPV, as models to understand the mechanisms of membrane fusion triggered by F protein.

Project 2: Understand the replication and gene expression of metapneumoviruses.

All viruses utilize host cell machinery to synthesize their own genetic materials. Upon entry into cells, the virus has to initiate replication and gene expression. Paramyxoviruses use a unique strategy for replication and gene expression. The active template for paramyxovirus replication is not the naked RNA genome but the protein and RNA complex. Viral genomic RNA is completely encapsidated by the nucleocapsid (N) protein to form an N-RNA complex. During RNA synthesis, the N-RNA template is recognized by viral RNA-dependent RNA polymerase (RdRp) that carries out two distinct processes: (i) transcription to yield 6-10 capped, methylated and polyadenylated messenger RNAs and (ii) replication to yield full-length antigenomic and subsequently genomic RNA.

Our lab uses hMPV and aMPV as models to understand the mechanisms by which the RdRp controls these two processes: replication and transcription. We will focus on the two major components of RdRp, the large protein catalytic subunit (L) and the cofactor phosphoprotein (P). We will use biochemical and genetic approaches to define functional domains in the RdRd that regulate replication and transcription. Disruption of these functional domains in the RdRp could potentially limit virus replication and thus attenuate the virus, or alternatively could be lethal to the virus. Therefore, a better understanding of replication and transcription control would facilitate the rational design and development of new vaccines and anti-viral drugs against these viruses.

Research interest II: Human norovirus and animal caliciviruses.

The Caliciviridae family includes a number of significant enteric viruses that cause gastroenteritis in humans and animals. Examples of these viruses include human norovirus, human sapovirus, porcine norovirus, and the newly discovered primate calicivirus (Tulane virus). Human norovirus is the leading cause of nonbacterial gastroenteritis worldwide, contributing to over 95% of all non-bacterial acute gastroenteritis each year, and more than 60% of all foodborne illnesses reported annually. However, human norovirus remains difficult to study because it cannot be grown in cell culture and it lacks a small animal model. Currently, there is no vaccine or antiviral drug against this virus.

Project 1: Develop practical prevention and control strategies against human norovirus.

Currently, there is no effective measure to control human norovirus. Our goal is to develop novel strategies to eliminate viral contamination in food, water, and the environment. We are interested in identifying effective sanitizers to remove viruses from food, equipment, and any contact surfaces; and identifying effective thermal and non-thermal processing technologies to inactivate viruses in foods and the environment.

Project 2: Understand the pathogenesis of human norovirus and primate calicivirus in a gnotobiotic pig model.

Recently, we found that Tulane virus, an enteric cultivable primate calicivirus that is genetically similar to human norovirus, replicates in gnotobiotic pigs. Similar to human norovirus, Tulane virus causes diarrhea and fecal viral shedding, and histological changes in pig intestines. Using gnotobiotic pigs as a model, we aim to understand the pathological and immunological aspects of human norovirus and primate calicivirus in vivo.

Project 3: Develop new vaccine candidates against human norovirus and other noncultivable caliciviruses.  

To date, there are no vaccines or anti-viral therapies for human norovirus. This is due in major part to the fact that human norovirus cannot be grown in cell culture. Generally, a live attenuated vaccine stimulates strong systemic immunity and provides durable protection. However, such a vaccine is not realistic for viruses that cannot grow in cell culture. In this situation, a vectored vaccine may be ideal. We are interested in developing non-segmented negative-strand RNA viruses (such as vesicular stomatitis virus, VSV) as vectors to deliver human norovirus virus-like particles (VLPs) to be used as a candidate live vaccine for human norovirus. Using a gnotobiotic pig model, we will examine the protective immune response against human norovirus infection using these vaccine candidates. VSV offers a number of advantages, such as safety, genetic stability, efficient expression of foreign genes, and induction of systemic immune responses. This recombinant system will provide a new avenue for the development of vaccines for non-cultivable caliciviruses.


Ongoing Research Support

  1. NIH/NIAID R01 (Li, PI; Niewiesk, Peeples, He, Co-Is) 02/01/2010 --01/30/2024

    “Messenger RNA capping and methylation in pneumoviruses.”

    The major goal of this project is to study the mechanism of messenger RNA processing in pneumoviruses.

  2. NIH/NIAID R01 (Li, Boyaka, He, Jiang, Multi-PIs)    03/01/2016 --02/30/2021 

    “A novel LAB-based norovirus vaccine.” 

    The major goal of this project is to develop a novel lactic acid bacteria (LAB)-based vaccine for human norovirus and to develop novel approaches to enhance immunity against human norovirus. 

  3. NIH/NIAID R01 (Boyaka, PI; Cormet-Boyaka, Li, Co-Is)    01/01/2020 --01/31/2024 

    “Targeting myeloid cells for regulation of alum-based immunity”

    The main goal of this project is to determine the role played by innate immune cells recruited/activated by alum at shaping adaptive immunity in the bloodstream and mucosal tissues.

  4. NIH/NIAID P01 (Peeples and Ramilo, PI; Niewiesk, Teng, Mejias, Li, co-PIs)    12/01/2015 --11/30/2021

    “Live attenuated human respiratory syncytial virus (RSV) vaccine with optimized safety and immunogenicity.” 

    The overall goal of this P01 is to develop a live, attenuated RSV vaccine by optimizing safety, genetics stability, and immunogenicity. 

  5. NIH/ NHGRI (He, PI; Li, Co-I)             11/01/2020-10/30-2021

    “Center for Dynamic RNA epitranscriptomes, COVID-19 administrative supplement”. 

    The main goal of this project is to map major RNA modifications in SARS-CoV-2 genome.