Development of improved vaccine cell lines against rotavirus

Seed Train Optimization in Microcarrier-Based Cell Culture Post In Situ Cell Detachment through Scale-Down Hybrid Modeling

Microcarrier-based cell culture is a commonly used method to facilitate the growth of anchorage-dependent cells like MA 104 for antigen manufacturing. However, conventionally, static cell culture is employed for cell propagation before seeding the production bioreactor with microcarriers (MCs). This study demonstrates the effective replacement of the conventional method by serial subculturing on MCs with in situ cell detachment under optimal conditions in closed culture units. This study proves that MA 104 can be subcultured at least five times on Cytodex 1 MC without the need for separating cells and MC after cell harvest. Process parameters impacting cell growth were studied post in situ cell detachment in a scaled-down model. Optimization, using augmented Design of Experiments (DoE) combined with hybrid modeling, facilitated rapid screening of the design space for critical process parameters (CPPs). Optimized conditions included an inoculation density of >16 cells/bead, 3.5-4.5 g/L of Cytodex 1, and a controlled agitation speed, starting at Njs (minimum agitation speed) for the first day with a maximum increase of 25% thereafter. With these design spaces for CPPs, a cell density of 2.6 ± 0.5 × 106 cells/mL was achieved after five days. This refined bioprocess methodology offers a reliable and efficient approach for seed training in stirred tank reactors, which is particularly beneficial for viral vaccine production.

Molecular engineering tools for the development of vaccines against infectious diseases: current status and future directions

INTRODUCTION

The escalating global changes have fostered conditions for the expansion and transmission of diverse biological factors, leading to the rise of emerging and reemerging infectious diseases. Complex viral infections, such as COVID-19, influenza, HIV, and Ebola, continue to surface, necessitating the development of effective vaccine technologies.

AREAS COVERED

This review article highlights recent advancements in molecular biology, virology, and genomics that have propelled the design and development of innovative molecular tools. These tools have promoted new vaccine research platforms and directly improved vaccine efficacy. The review summarizes the cutting-edge molecular engineering tools used in creating novel vaccines and explores the rapidly expanding molecular tools landscape and potential directions for future vaccine development.

EXPERT OPINION

The strategic application of advanced molecular engineering tools can address conventional vaccine limitations, enhance the overall efficacy of vaccine products, promote diversification in vaccine platforms, and form the foundation for future vaccine development. Prioritizing safety considerations of these novel molecular tools during vaccine development is crucial.

Comparison of IgA Antibody Titer Induced by Human-Bovine Rotavirus Candidate Vaccine with Bovine Rotavirus and Rotarix

Rotavirus (RV) is the most common cause of acute gastroenteritis in early childhood worldwide. Gastroenteritis is a preventable disease by the vaccine, and vigorous efforts were made to produce attenuated oral rotavirus vaccines. In recent years, despite the existence of three types of live attenuated rotavirus vaccines, several countries, such as China and Vietnam, have intended to produce indigenous vaccines based on rotavirus serotypes circulating among their population. In this study, the immunogenicity of homemade human-bovine reassortant RV candidate vaccine was tested in an animal model. Rabbits were randomly distributed into eight experimental groups with three animals per group. Afterward, three rabbits in each test group designated as P1, P2, and P3 were experimentally inoculated with the 106, 107, and 108 tissue culture infectious dose 50 (TCID50) of the reassortant virus, respectively. The N1 group received the reassortant rotavirus vaccine containing 107 TCID50+zinc. The N2, N3, and N4 groups received rotavirus vaccine strain, RV4 human rotavirus, and bovine rotavirus strain, respectively, and the control group received phosphate-buffered saline. It is noteworthy that three rabbits have been included in each group. The IgA total antibody titer was measured and evaluated by non-parametric Mann-Whitney and Kruskal-Wallis tests. The antibody titer produced in the studied groups did not significantly differ. The candidate vaccine showed immunogenicity, protectivity, stability, and safety. The findings of this study indicated a critical role of IgA production, which can induce immunity against a gastroenteritis viral pathogen. Regardless of purification, candidate reassortant vaccine and cell adapted animal strains could be used as a vaccine candidate for production.

An overview: CRISPR/Cas-based gene editing for viral vaccine development

INTRODUCTION

: Gene-editing technology revolutionized vaccine manufacturing and offers a variety of benefits over traditional vaccinations, such as improved immune response, higher production rate, stability, precise immunogenic activity, and fewer adverse effects. The more recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/associated protein 9 (Cas9) system has become the most widely utilized technology based on its efficiency, utility, flexibility, versatility, ease of use, and cheaper compared to other gene-editing techniques. Considering its wider scope for genomic modification, CRISPR/Cas9-based technology's potential is explored for vaccine development.

AREAS COVERED

: In this review, we will address the recent advances in the CRISPR/Cas system for the development of vaccines and viral vectors for delivery. In addition, we will discuss strategies for the development of the vaccine, as well as the limitations and future prospects of the CRISPR/Cas system.

EXPERT OPINION

: Human and animal viruses have been exposed to antiviral CRISPR/Cas9-based engineering to prevent infection, which uses knockout, knock-in, gene activation/deactivation, RNA targeting, and editing cell lines strategies for gene editing of viruses. Because of that CRISPR/Cas system is used to boost the vaccine production yield by removing unwanted genes that cause disease or are required for viral infection.

Repurposing Probenecid to Inhibit SARS-CoV-2, Influenza Virus, and Respiratory Syncytial Virus (RSV) Replication

Viral replication and transmissibility are the principal causes of endemic and pandemic disease threats. There remains a need for broad-spectrum antiviral agents. The most common respiratory viruses are endemic agents such as coronaviruses, respiratory syncytial viruses, and influenza viruses. Although vaccines are available for SARS-CoV-2 and some influenza viruses, there is a paucity of effective antiviral drugs, while for RSV there is no vaccine available, and therapeutic treatments are very limited. We have previously shown that probenecid is safe and effective in limiting influenza A virus replication and SARS-CoV-2 replication, along with strong evidence showing inhibition of RSV replication in vitro and in vivo. This review article will describe the antiviral activity profile of probenecid against these three viruses.

MicroRNAs affect GPCR and Ion channel genes needed for influenza replication

Influenza virus causes seasonal epidemics and sporadic pandemics resulting in morbidity, mortality, and economic losses worldwide. Understanding how to regulate influenza virus replication is important for developing vaccine and therapeutic strategies. Identifying microRNAs (miRs) that affect host genes used by influenza virus for replication can support an antiviral strategy. In this study, G-protein coupled receptor (GPCR) and ion channel (IC) host genes in human alveolar epithelial (A549) cells used by influenza virus for replication (Orr-Burks et al., 2021) were examined as miR target genes following A/CA/04/09- or B/Yamagata/16/1988 replication. Thirty-three miRs were predicted to target GPCR or IC genes and their miR mimics were evaluated for their ability to decrease influenza virus replication. Paired miR inhibitors were used as an ancillary measure to confirm or not the antiviral effects of a miR mimic. Fifteen miRs lowered influenza virus replication and four miRs were found to reduce replication irrespective of virus strain and type differences. These findings provide evidence for novel miR disease intervention strategies for influenza viruses.

Perspectives for the optimization and utility of the rotavirus reverse genetics system

Following Kobayashi and colleagues' seminal paper in 20171, in the past four years the rotavirus (RV) field has witnessed a burst in research and publications based on the use of a fully plasmid-based RV reverse genetics systems and subsequent modifications2,3. However, in most cases, the rotaviral strain under interrogation has been the prototypic simian RV SA11-L2 strain (G3P[2]). Of note, a variety of other weakly-to-modestly replication-competent animal and human RV strains, bioluminescent and fluorescent reporter viruses, and clinical isolates of human RVs have proved hard or impossible to rescue using the original reverse genetics system2,4, highlighting a critical need to further enhance the recovery efficiency and expand the rescue tool kit. A number of further modifications of the initial reverse genetics system have enabled the rescue of other RV strains such as the human RV KU and CDC-9 strains, and a murine RV D6/2-like strain4,5. Here, we discuss future possible modifications of existing RV reverse genetics systems to further increase efficiency based on past experience with the improvement of influenza A virus recovery. The development of RV to accommodate the insertion and expression of heterologous sequences has substantial potential in the design of next-generation RV vaccine candidates and enteric viral vectors.

CRISPR-Csy4-Mediated Editing of Rotavirus Double-Stranded RNA Genome

CRISPR-nucleases have been widely applied for editing cellular and viral genomes, but nuclease-mediated genome editing of double-stranded RNA (dsRNA) viruses has not yet been reported. Here, by engineering CRISPR-Csy4 nuclease to localize to rotavirus viral factories, we achieve the nuclease-mediated genome editing of rotavirus, an important human and livestock pathogen with a multisegmented dsRNA genome. Rotavirus replication intermediates cleaved by Csy4 is edited through the formation of precise deletions in the targeted genome segments in a single replication cycle. Using CRISPR-Csy4-mediated editing of rotavirus genome, we label the products of rotavirus secondary transcription made by newly assembled viral particles during rotavirus replication, demonstrating that this step largely contributes to the overall production of viral proteins. We anticipate that the nuclease-mediated cleavage of dsRNA virus genomes will promote an advanced level of understanding of viral replication and host-pathogen interactions, also offering opportunities to develop therapeutics.

Application of CRISPR-Cas9 Editing for Virus Engineering and the Development of Recombinant Viral Vaccines

CRISPR-Cas technology, discovered originally as a bacterial defense system, has been extensively repurposed as a powerful tool for genome editing for multiple applications in biology. In the field of virology, CRISPR-Cas9 technology has been widely applied on genetic recombination and engineering of genomes of various viruses to ask some fundamental questions about virus-host interactions. Its high efficiency, specificity, versatility, and low cost have also provided great inspiration and hope in the field of vaccinology to solve a series of bottleneck problems in the development of recombinant viral vaccines. This review highlights the applications of CRISPR editing in the technological advances compared to the traditional approaches used for the construction of recombinant viral vaccines and vectors, the main factors affecting their application, and the challenges that need to be overcome for further streamlining their effective usage in the prevention and control of diseases. Factors affecting efficiency, target specificity, and fidelity of CRISPR-Cas editing in the context of viral genome editing and development of recombinant vaccines are also discussed.

Experimental Methods to Study the Pathogenesis of Human Enteric RNA Viruses

Every year, millions of children are infected with viruses that target the gastrointestinal tract, causing acute gastroenteritis and diarrheal illness. Indeed, approximately 700 million episodes of diarrhea occur in children under five annually, with RNA viruses norovirus, rotavirus, and astrovirus serving as major causative pathogens. Numerous methodological advancements in recent years, including the establishment of novel cultivation systems using enteroids as well as the development of murine and other animal models of infection, have helped provide insight into many features of viral pathogenesis. However, many aspects of enteric viral infections remain elusive, demanding further study. Here, we describe the different in vitro and in vivo tools available to explore different pathophysiological attributes of human enteric RNA viruses, highlighting their advantages and limitations depending upon the question being explored. In addition, we discuss key areas and opportunities that would benefit from further methodological progress.

G-Protein-Coupled Receptor and Ion Channel Genes Used by Influenza Virus for Replication

Influenza virus causes epidemics and sporadic pandemics resulting in morbidity, mortality, and economic losses. Influenza viruses require host genes to replicate. RNA interference (RNAi) screens can identify host genes coopted by influenza virus for replication. Targeting these proinfluenza genes can provide therapeutic strategies to reduce virus replication. Nineteen proinfluenza G-protein-coupled receptor (GPCR) and 13 proinfluenza ion channel genes were identified in human lung (A549) cells by use of small interfering RNAs (siRNAs). These proinfluenza genes were authenticated by testing influenza virus A/WSN/33-, A/CA/04/09-, and B/Yamagata/16/1988-infected A549 cells, resulting in the validation of 16 proinfluenza GPCR and 5 proinfluenza ion channel genes. These findings showed that several GPCR and ion channel genes are needed for the production of infectious influenza virus. These data provide potential targets for the development of host-directed therapeutic strategies to impede the influenza virus productive cycle so as to limit infection.IMPORTANCE Influenza epidemics result in morbidity and mortality each year. Vaccines are the most effective preventive measure but require annual reformulation, since a mismatch of vaccine strains can result in vaccine failure. Antiviral measures are desirable particularly when vaccines fail. In this study, we used RNAi screening to identify several GPCR and ion channel genes needed for influenza virus replication. Understanding the host genes usurped by influenza virus during viral replication can help identify host genes that can be targeted for drug repurposing or for the development of antiviral drugs. The targeting of host genes is refractory to drug resistance generated by viral mutations, as well as providing a platform for the development of broad-spectrum antiviral drugs.

In Vitro Evaluation of Anti-Rift Valley Fever Virus, Antioxidant and Anti-Inflammatory Activity of South African Medicinal Plant Extracts

Rift valley fever virus (RVFV) is a mosquito-borne virus endemic to sub-Saharan African countries, and the first sporadic outbreaks outside Africa were reported in the Asia-Pacific region. There are no approved therapeutic agents available for RVFV; however, finding an effective antiviral agent against RVFV is important. This study aimed to evaluate the antiviral, antioxidant and anti-inflammatory activity of medicinal plant extracts. Twenty medicinal plants were screened for their anti-RVFV activity using the cytopathic effect (CPE) reduction method. The cytotoxicity assessment of the extracts was done before antiviral screening using the MTT assay. Antioxidant and reactive oxygen/nitrogen species' (ROS/RNS) inhibitory activity by the extracts was investigated using non-cell-based and cell-based assays. Out of twenty plant extracts tested, eight showed significant potency against RVFV indicated by a decrease in tissue culture infectious dose (TCID50) < 105. The cytotoxicity of extracts showed inhibitory concentrations values (IC50) > 200 µg/mL for most of the extracts. The antioxidant activity and anti-inflammatory results revealed that extracts scavenged free radicals exhibiting an IC50 range of 4.12-20.41 µg/mL and suppressed the production of pro-inflammatory mediators by 60-80% in Vero cells. This study demonstrated the ability of the extracts to lower RVFV viral load and their potency to reduce free radicals.

Cell Cultures for Virology: Usability, Advantages, and Prospects

Virus detection in natural and clinical samples is a complicated problem in research and diagnostics. There are different approaches for virus isolation and identification, including PCR, CRISPR/Cas technology, NGS, immunoassays, and cell-based assays. Following the development of genetic engineering methods, approaches that utilize cell cultures have become useful and informative. Molecular biology methods allow increases in the sensitivity and specificity of cell cultures for certain viruses and can be used to generate reporter cell lines. These cell lines express specific reporter proteins (e.g., GFP, luciferase, and CAT) in response to virus infection that can be detected in a laboratory setting. The development of genome editing and synthetic biology methods has given rise to new perspectives regarding the design of virus reporter systems in cell cultures. This review is aimed at describing both virology methods in general and examples of the development of cell-based methods that exist today.

Vero cell upstream bioprocess development for the production of viral vectors and vaccines

The Vero cell line is considered the most used continuous cell line for the production of viral vectors and vaccines. Historically, it is the first cell line that was approved by the WHO for the production of human vaccines. Comprehensive experimental data on the production of many viruses using the Vero cell line can be found in the literature. However, the vast majority of these processes is relying on the microcarrier technology. While this system is established for the large-scale manufacturing of viral vaccine, it is still quite complex and labor intensive. Moreover, scale-up remains difficult and is limited by the surface area given by the carriers. To overcome these and other drawbacks and to establish more efficient manufacturing processes, it is a priority to further develop the Vero cell platform by applying novel bioprocess technologies. Especially in times like the current COVID-19 pandemic, advanced and scalable platform technologies could provide more efficient and cost-effective solutions to meet the global vaccine demand. Herein, we review the prevailing literature on Vero cell bioprocess development for the production of viral vectors and vaccines with the aim to assess the recent advances in bioprocess development. We critically underline the need for further research activities and describe bottlenecks to improve the Vero cell platform by taking advantage of recent developments in the cell culture engineering field.

A pooled genome-wide screening strategy to identify and rank influenza host restriction factors in cell-based vaccine production platforms

Cell-derived influenza vaccines provide better protection and a host of other advantages compared to the egg-derived vaccines that currently dominate the market, but their widespread use is hampered by a lack of high yield, low cost production platforms. Identification and knockout of innate immune and metabolic restriction factors within relevant host cell lines used to grow the virus could offer a means to substantially increase vaccine yield. In this paper, we describe and validate a novel genome-wide pooled CRISPR/Cas9 screening strategy that incorporates a reporter virus and a FACS selection step to identify and rank restriction factors in a given vaccine production cell line. Using the HEK-293SF cell line and A/PuertoRico/8/1934 H1N1 influenza as a model, we identify 64 putative influenza restriction factors to direct the creation of high yield knockout cell lines. In addition, gene ontology and protein complex enrichment analysis of this list of putative restriction factors offers broader insights into the primary host cell determinants of viral yield in cell-based vaccine production systems. Overall, this work will advance efforts to address the public health burden posed by influenza.

Vero Cells as a Mammalian Cell Substrate for Human Norovirus

Human norovirus (HuNoV) is a principal cause of acute gastroenteritis worldwide, particularly in developing countries. Its global prevalence is underscored by more serious morbidity and some mortality in the young (<5 years) and the elderly. To date, there are no licensed vaccines or approved therapeutics for HuNoV, mostly because there are limited cell culture systems and small animal models available. Recently described cell culture systems are not ideal substrates for HuNoV vaccine development because they are not clonal or only support a single strain. In this study, we show Vero cell-based replication of two pandemic GII.4 HuNoV strains and one GII.3 strain and confirm exosome-mediated HuNoV infection in Vero cells. Lastly, we show that trypsin addition to virus cultures or disruption of Vero cell host genes can modestly increase HuNoV replication. These data provide support for Vero cells as a cell culture model for HuNoV.

Gene-edited vero cells as rotavirus vaccine substrates

Background

Rotavirus (RV) is a leading cause of severe gastroenteritis globally and can cause substantial morbidity associated with gastroenteritis in children <5 years of age. Orally administered live-attenuated RV vaccines offer protection against disease but vaccination efforts have been hampered by high manufacturing costs and the need to maintain a cold chain.

Methods

A subset of Vero cell host genes was identified by siRNA that when knocked down increased RV replication and these anti-viral host genes were individually deleted using CRISPR-Cas9.

Results

Fully-sequenced gene knockout Vero cell substrates were assessed for increased RV replication and RV vaccine antigen expression compared to wild type Vero cells. The results showed that RV replication and antigen production were logs higher in Vero cells having an EMX2 gene deletion compared to other Vero cell substrates tested.

Conclusions

We used siRNAs to screen for host genes that negatively affected RV replication, then CRISPR-Cas9 gene editing to delete select genes. The gene editing led to the development of enhanced RV vaccine substrates supporting a potential path forward for improving RV vaccine production.

Enhancing viral vaccine production using engineered knockout vero cell lines - A second look

The global adoption of vaccines to combat disease is hampered by the high cost of vaccine manufacturing. The work described herein follows two previous publications (van der Sanden et al., 2016; Wu et al., 2017) that report a strategy to enhance poliovirus and rotavirus vaccine production through genetic modification of the Vero cell lines used in large-scale vaccine manufacturing. CRISPR/Cas9 gene editing tools were used to knockout Vero target genes previously shown to play a role in polio- and rotavirus production. Subsequently, small-scale models of current industry manufacturing systems were developed and adopted to assess the increases in polio- and rotavirus output by multiple stable knockout cell lines. Unlike previous studies, the Vero knockout cell lines failed to achieve desired target yield increases. These findings suggest that additional research will be required before implementing the genetically engineered Vero cell lines in the manufacturing process for polio- and rotavirus vaccines to be able to supply vaccines at reduced prices.

A universal mammalian vaccine cell line substrate

Using genome-wide small interfering RNA (siRNA) screens for poliovirus, influenza A virus and rotavirus, we validated the top 6 gene hits PV, RV or IAV to search for host genes that when knocked-down (KD) enhanced virus permissiveness and replication over wild type Vero cells or HEp-2 cells. The enhanced virus replication was tested for 12 viruses and ranged from 2-fold to >1000-fold. There were variations in virus-specific replication (strain differences) across the cell lines examined. Some host genes (CNTD2, COQ9, GCGR, NDUFA9, NEU2, PYCR1, SEC16G, SVOPL, ZFYVE9, and ZNF205) showed that KD resulted in enhanced virus replication. These findings advance platform-enabling vaccine technology, the creation of diagnostic cells substrates, and are informative about the host mechanisms that affect virus replication in mammalian cells.

Knocking down the obstacles to functional genomics data sharing

This week, Scientific Data published a collection of eight papers that describe datasets from high-throughput functional genomics screens, primarily utilizing RNA interference (RNAi). The publications explore host-pathogen dependencies, innate immune response, disease pathways, and cell morphology and motility at the genome-level. All data, including raw images from the high content screens, are publically available in PubChem BioAssay, figshare, Harvard Dataverse or the Image Data Resource (IDR). Detailed data descriptors enable use of these data for analysis algorithm design, machine learning, data comparisons, as well as generating new scientific hypotheses.