pH inactivation of SARS-CoV-2 and SARS-CoV in virus spiked protein A eluates from a mAb purification process

Biopharmaceutical manufacturing processes may include a low pH treatment step as a means of inactivating enveloped viruses. Small scale virus clearance studies are routinely performed using model enveloped viruses such as murine leukemia virus to assess inactivation at the pH range used in the downstream manufacturing process. Further, as a means of bioburden reduction, chromatography resins may be cleaned and stored using sodium hydroxide and this can also inactivate viruses. The susceptibility of SARS-CoV-2 and SARS-CoV to low pH conditions using protein A eluate derived material from a monoclonal antibody production process as well as high pH cleaning conditions was addressed. SARS-CoV-2 was effectively inactivated at pH 3.0, moderately inactivated at pH 3.4, but not inactivated at pH 3.8. Low pH was less effective at inactivating SARS-CoV. Both viruses were inactivated at a high pH of ca.13.4. These studies provide important information regarding the effectiveness of viral clearance and inactivation steps of novel coronaviruses when compared to other enveloped viruses.

Vitamin D3 can effectively and rapidly clear largemouth bass ranavirus by immunoregulation

Largemouth bass ranavirus (LMBV) is a highly destructive pathogen that causes significant mortality rates among largemouth bass populations. Unfortunately, there is a dearth of drug development efforts specifically aimed at treating LMBV. To address this, our study sought to investigate the potential effectiveness of incorporating varying doses of VD3 into the diet as a treatment for LMBV. Through qRT-PCR and semi-qPCR, we observed significant suppression and clearance of LMBV pathogens in largemouth bass fed with 15000 IU/Kg and 20000 IU/Kg of VD3 within 14 days. In addition, VD3 treatment significantly increased the expression levels of key immune-related genes such as IL-1β, IFN-γ, Mx, and IgM. Encouragingly, we observed that VD3 significantly increased antioxidant and immune activities such as TSOD, TAOC and C3 in serum and maintained total protein levels. Additionally, tissue pathology sections highlighted a dose-dependent relationship between VD3 supplementation and tissue damage, with the 15000 IU and 20000 IU groups exhibiting minimal damage. In conclusion, a reasonable concentration of VD3 effectively reduced LMBV replication and tissue damages, while improved immune-related genes expression and serum biochemical indices. These findings declare the considerable therapeutic potential of VD3 supplementation for combating LMBV disease and provide an alternative treatment option for fish farming.

Delayed SARS-COV-2 clearance in infected persons in Ghana

Objective

This study aimed to determine the duration of SARS-CoV-2 clearance in persons in Ghana. The research question was whether the duration of virus clearance in Ghana matched the 14 days recommended by the World Health Organization (WHO); this had direct implications for transmission, which was key in managing the COVID-19 pandemic.

Design

This was a retrospective analytical study.

Setting

All facilities that submitted clinical specimens to Noguchi Memorial Institute for Medical Research (NMIMR) for SARS-CoV-2 diagnosis between March to June 2020 were included in the study.

Interventions

Samples from 480 persons who tested positive for SARS-CoV-2 by RT-PCR from March to June 2020 at NMIMR and submitted at least two follow-up samples were retrospectively analysed. Individuals with two consecutive negative RT-PCR retesting results were considered to have cleared SARS-CoV-2.

Results

The median time from the initial positive test to virus clearance was 20 days (IQR: 5-56 days). This was six days longer than the WHO-recommended 14 days, after which infected persons could be de-isolated. Sputum and nasopharyngeal swabs proved more sensitive for detecting viral RNA as the infection progressed. At a significance level of 0.05, age and sex did not seem to influence the time to SARS-CoV-2 clearance.

Conclusions

The median time to SARS-CoV-2 clearance in this study was 20 days, suggesting that SARS-CoV-2 infected persons in Ghana take longer to clear the virus. This finding calls for further investigations into whether patients who remain PCR positive continue to be infectious and inform isolation practices in Ghana.

Funding

The study was supported by the Ministry of Health/ Ghana Health Service through the provision of laboratory supplies, the US Naval Medical Research Unit #3, the World Health Organization, the Jack Ma Foundation and the Virology Department of Noguchi Memorial Institute for Medical Research, University of Ghana. Research projects within Noguchi Memorial Institute for Medical Research contributed reagents and laboratory consumables. However, the authors alone are responsible for the contents of this manuscript.

Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients

COVID-19 has emerged as a global pandemic, challenging the world's economic and health systems. Human oral microbiota comprises the second largest microbial community after the gut microbiota and is closely related to respiratory tract infections; however, oral microbiomes of patients who have recovered from COVID-19 have not yet been thoroughly studied. Herein, we compared the oral bacterial and fungal microbiota after clearance of SARS-CoV-2 in 23 COVID-19 recovered patients to those of 29 healthy individuals. Our results showed that both bacterial and fungal diversity were nearly normalized in recovered patients. The relative abundance of some specific bacteria and fungi, primarily opportunistic pathogens, decreased in recovered patients (RPs), while the abundance of butyrate-producing organisms increased in these patients. Moreover, these differences were still present for some organisms at 12 months after recovery, indicating the need for long-term monitoring of COVID-19 patients after virus clearance.

Using Sensitivity Analysis to Simplify the Virus Safety Factor Calculation in the Manufacture of Biopharmaceuticals

Virus safety of biopharmaceuticals produced in cells of animal origin is governed by regulatory guidelines. It is ensured through raw material controls, cell substrate testing, and evaluation of the purification process for virus clearance capability. An additional control for cell lines that contain endogenous viruses is the virus safety factor (VSF) calculation, to demonstrate that the virus clearance exceeds the amount of potential endogenous virus in a dose of product. Product-specific input data (product titer, process yield, intended dose, purification process virus clearance capability, and the measured titer of endogenous virus produced by the cells) are typically used for the calculation. A wide range of relevant data was obtained from the production of monoclonal antibodies in Chinese Hamster Ovary (CHO) cells, and a sensitivity analysis was performed by using Monte Carlo simulations to determine which input data had the most significant impact on the range and distribution of the VSF. The sensitivity analysis suggested that the VSF calculation can be streamlined to include virus clearance capability, the endogenous virus titer, and dose while excluding product titer and process yield. Furthermore, the simulated VSF exceeded 4 log₁₀ in 96% of the simulations, providing a high level of assurance of virus safety for antibodies produced in CHO cells and purified within specified operational parameters.

Long-term antibody production and viremia in American mink (Neovison vison) challenged with Aleutian mink disease virus

Background

Selecting American mink (Neovison vison) for tolerance to Aleutian mink disease virus (AMDV) has gained popularity in recent years, but data on the outcomes of this activity are scant. The objectives of this study were to determine the long-term changes in viremia, seroconversion and survival in infected mink. Mink were inoculated intranasally with a local isolate of Aleutian mink disease virus (AMDV) over 4 years (n = 1742). The animals had been selected for tolerance to AMDV for more than 20 years (TG100) or were from herds free of AMDV (TG0). The progenies of TG100 and TG0, and their crosses with 25, 50 and 75% tolerance ancestry were also used. Blood samples were collected from each mink up to 14 times until 1211 days post-inoculation (dpi) and were tested for viremia by PCR and for anti-AMDV antibodies by counter-immunoelectrophoresis (CIEP). Viremia and CIEP status were not considered when selecting replacements. Low-performing animals were pelted and the presence of antibodies in their blood and antibody titer were measured by CIEP, and viremia and viral DNA in seven organs (n = 936) were tested by PCR.

Results

The peak incidences of viremia (66.7%) and seropositivity (93.5%) were at 35 dpi. The incidence of viremia decreased over time while the incidence of seroconversion increased. The least-squares means of the incidence of PCR positive of lymph node (0.743) and spleen (0.656) were significantly greater than those of bone marrow, liver, kidneys, lungs and small intestine (0.194 to 0.342). Differences in tolerant ancestry were significant for every trait measured. Incidences of viremia over time, terminal viremia, seropositivity over time, AMDV DNA in organs and antibody titer were highest in the susceptible groups (TG0 or TG25) and lowest in the tolerant groups (TG100 or TG75).

Conclusion

Previous history of selection for tolerance resulted in mink with reduced viral replication and antibody titer. Viremia had a negative effect and antibody production had a positive effect on survival and productivity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03462-7.

Development of a transient inline spiking system for evaluating virus clearance in continuous bioprocessing -- Proof of concept for virus filtration

The development of continuous/connected bioprocesses requires new approaches for viral clearance validation, both for specific unit operations and for the overall process. In this study, we have developed a transient inline spiking system that can be used to evaluate virus clearance at distinct time points during prolonged operation of continuous bioprocesses. The proof of concept for this system was demonstrated by evaluating the viral clearance for a virus filtration step, both with and without a prefilter upstream of the virus filter. The residence time distribution was evaluated using a previously identified non-interacting fluorescent tracer, while viral clearance was evaluated from measurements of the virus titer in samples obtained downstream of the virus filter. The measured log reduction values (LRV) for ϕX174, Minute Virus of Mice (MVM), Xenotropic Murine Leukemia Virus (XMuLV), and a non-infectious Mock Virus Particle (MVP) were all within 0.5 logs of those obtained using a traditional batch virus challenge for both model and real-world process streams (LRV between 2.2 and 3.4 for ϕX174 using a single layer of virus filter). The results demonstrate the effectiveness of transient inline spiking to validate the virus clearance capabilities in continuous bioprocessing, an essential element for the adoption of these processes for products made using mammalian cell lines. This article is protected by copyright. All rights reserved.

Broad virus inactivation using inorganic micro/nano-particulate materials

Inorganic materials can provide a set of tools to decontaminate solid, liquid or air containing viral particles. The use of disinfectants can be limited or not practical in scenarios where continuous cleaning is not feasible. Physicochemical differences between viruses raise the need for effective formulations for all kind of viruses. In the present work we describe two types of antimicrobial inorganic materials: i) a novel soda-lime glass (G3), and ii) kaolin containing metals nanoparticles (Ag or CuO), as materials to disable virus infectivity. Strong antiviral properties can be observed in G3 glass, and kaolin-containing nanoparticle materials showing a reduction of viral infectivity close to 99%. in the first 10 ​min of contact of vesicular stomatitis virus (VSV). A potent virucidal activity is also present in G3 and kaolin containing Ag or CuO nanoparticles against all kinds of viruses tested, reducing more than 99% the amount of HSV-1, Adenovirus, VSV, Influenza virus and SARS-CoV-2 exposed to them. Virucidal properties could be explained by a direct interaction of materials with viruses as well as inactivation by the presence of virucidal elements in the material lixiviates. Kaolin-based materials guarantee a controlled release of active nanoparticles with antiviral activity. Current coronavirus crisis highlights the need for new strategies to remove viruses from contaminated areas. We propose these low-cost inorganic materials as useful disinfecting antivirals in the actual or future pandemic threats.

Lower Serum Angiotensin-Converting Enzyme Level in Relation to Hyperinflammation and Impaired Antiviral Immune Response Contributes to Progression of COVID-19 Infection

INTRODUCTION

As a homologue of the angiotensin-converting enzyme (ACE), angiotensin-converting enzyme 2 (ACE2) has been identified as the main receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) invasion. We aimed to investigate the role of serum ACE in predicting the coronavirus disease 2019 (COVID-19) disease progression and the underlying mechanisms.

METHODS

We retrospectively enrolled 120 patients with confirmed COVID-19 who underwent serum ACE detection on admission. The clinical characteristics and laboratory findings during hospitalization were evaluated dynamically to identify the potential risk factors for disease progression.

RESULTS

ACE level was demonstrated as one of the independent risk factors. Patients with ACE level ≤ 33.5 U/L showed a higher cumulative virus RNA detection rate, elevated pro-inflammatory mediators levels, declined lymphocyte count, and decreased SARS-CoV-2-specific antibodies than those with ACE level > 33.5 U/L.

CONCLUSION

Lower serum ACE levels in relation to delayed virus elimination, hyperinflammatory condition, and impaired host antiviral immune responses contribute to disease progression of COVID-19.

Corticosteroid therapy is associated with the delay of SARS-CoV-2 clearance in COVID-19 patients

The impact of corticosteroid treatment on virological course of coronavirus disease 2019 (COVID-19) patients remains unclear. This study aimed to explore the association between corticosteroid and viral clearance in COVID-19. The clinical data of COVID-19 patients from 10 hospitals of Jiangsu, China, were retrospectively collected. Cox regression and Kaplan-Meier analysis were used to analyze the adverse factors of virus clearance. Of the 309 COVID-19 patients, eighty-nine (28.8%) patients received corticosteroid treatment during hospitalization. Corticosteroid group showed higher C-reactive protein (median 11.1 vs. 7.0 mg/l, P = 0.018) and lower lymphocytes (median 0.9 vs. 1.4 × 109/l, P < 0.001) on admission. Fever (93.3% vs. 65.0%, P < 0.001) and cough (69.7% vs. 57.3%, P = 0.043) were more common in corticosteroid group. The proportions of patients with severe illness (34.8% vs. 1.8%, P < 0.001), respiratory failure (25.8% vs. 1.4%, P < 0.001), acute respiratory distress syndrome (4.5% vs. 0%, P = 0.002), and admission to ICU (20.2% vs. 0.9%, P < 0.001) were significantly higher in corticosteroid group than non-corticosteroid group. The duration of virus clearance (median 18.0 vs. 16.0 days, P < 0.001) and hospitalization (median 17.0 vs. 15.0 days, P < 0.001) were also significantly longer in corticosteroid group than non-corticosteroid group. Treated with corticosteroid (Hazard ratio [HR], 0.698; 95% confidence interval [CI], 0.512 to 0.951; P = 0.023) was an adverse factor of the clearance of SARS-CoV-2, especially for male patients (HR, 0.620; 95% CI, 0.408 to 0.942; P = 0.025). The cumulative probability of SARS-CoV-2 clearance was lower in corticosteroid group (P < 0.001). Corticosteroid treatment may delay the SARS-CoV-2 clearance of COVID-19 patients and should be used with cautions.

Proceedings of the 2017 Viral Clearance Symposium Session 5: Facility Risk Mitigation

The discussion on facility risk mitigation was included for the first time at the 2017 Viral Clearance Symposium. A few topics were discussed in this session, including sanitization/cleaning against viruses, viral segregation, as well as the definition of a "functionally closed" system.Virus inactivation by disinfectants is critical for the biotechnology industry. The efficacy can differ, depending on whether applied to surfaces, in solutions, or in gas phases, as well as the respective disinfectants (i.e., peracetic acid/hydrogen peroxide-based, hypochlorite-based, or glutaraldehyde-based).Most equipment used in the biotech industry can be cleaned or sanitized by alkaline solutions. Many of these methods were studied regarding their virus reduction potential and were defined considering alkaline concentration, time, and temperature.Virus clearance may be compromised if cross contamination or carryover happens from an early step with potentially a higher level of virus to a later step in the purification process (i.e., after virus removal or inactivation). Critical potential carryover (V_cpc) is defined as the volume of carryover that will significantly affect the overall virus clearance of a purification process. Based on the evaluation of critical potential carryover, mitigation actions can be introduced to avoid such carryover.Appropriate segregation within manufacturing facilities is required by regulators and utilized by manufacturers to ensure that the final product has appropriate safety margins. However, consensus around basic definitions and approaches related to facility segregation is lacking. To address this gap, the member companies of the Consortium on Adventitious Agent Contamination in Biomanufacturing have begun a project with the goal of developing a definition for a "functionally closed" manufacturing system.LAY ABSTRACT: The discussion on facility risk mitigation was included for the first time at the 2017 Viral Clearance Symposium. The topics discussed in this session included sanitization/cleaning against viruses, viral segregation, as well as the definition of a "functionally closed" system.Virus inactivation by disinfectants is critical for the biotechnology industry. The efficacy can differ, depending on whether applied to surfaces, in solutions, or in gas phases, as well as the respective disinfectants.Most equipment used in the biotech industry can be cleaned or sanitized by alkaline solutions. Many of these methods were studied regarding their virus reduction potential and were defined considering alkaline concentration, time, and temperature.Virus clearance may be compromised if cross contamination or carryover happens from an early step with potentially a higher level of virus to a later step in the purification process (i.e., after virus removal or inactivation).Regarding segregation within manufacturing facilities, the member companies of the Consortium on Adventitious Agent Contamination in Biomanufacturing have begun a project with the goal of developing a definition for a "functionally closed" manufacturing system. During this session, the current definition was discussed.

Meeting Report: 2013 PDA Virus & TSE Safety Forum

The report provides a summary of the presentations and discussions at the Virus & TSE Safety Forum 2013 organized by the Parenteral Drug Association (PDA) and held in Berlin, Germany, from June 4 to 6, 2013. The conference was accompanied by a workshop, "Virus Spike Preparations and Virus Removal by Filtration: New Trends and Developments". The presentations and the discussion at the workshop are summarized in a separate report that will be published in this issue of the journal as well. As with previous conferences of this series, the PDA Virus & TSE Safety Forum 2013 provided again an excellent opportunity to exchange information and opinions between the industry, research organizations, and regulatory bodies. Updates on regulatory considerations related to virus and transmissible spongiform encephalopathy (TSE) safety of biopharmaceuticals were provided by agencies of the European Union (EU), the United States (US), and Singapore. The epidemiology and detection methods of new emerging pathogens like hepatitis E virus and parvovirus (PARV 4) were exemplified, and the risk of contamination of animal-derived raw materials like trypsin was considered in particular. The benefit of using new sequence-based virus detection methods was discussed. Events of bioreactor contaminations in the past drew the attention to root cause investigations and preventive actions, which were illustrated by several examples. Virus clearance data of specific unit operations were provided; the discussion focused on the mechanism of virus clearance and on the strategic concept of viral clearance integration. As in previous years, the virus safety section was followed by a TSE section that covered recent scientific findings that may influence the risk assessment of blood and cell substrates. These included the realization that interspecies transmission of TSE by blood components in sheep is greater than predicted by assays in transgenic mice. Also, the pathogenesis and possibility of productive TSE infection of cell substrates were considered, and cell-based assays that may be suitable for use in TSE clearance studies were discussed. The current report provides an overview about the outcomes of the 2013 PDA Virus & TSE Safety Forum, a unique event in this field.

Meeting Report: 2015 PDA Virus & TSE Safety Forum

The report provides a summary of the presentations at the Virus & TSE Safety Forum 2015 organized by the Parenteral Drug Association (PDA) and held in Cascais, Portugal, from 9 to 11 June, 2015. As with previous conferences of this series, the PDA Virus & TSE Safety Forum 2015 provided an excellent forum for the exchange of information and opinions between the industry, research organizations, and regulatory bodies. Regulatory updates on virus and TSE safety aspects illustrating current topics of discussion at regulatory agencies in Europe and the United States were provided; the conference covered emerging viruses and new virus detection systems that may be used for the investigation of human pathogenic viruses as well as the virus safety of cell substrates and of raw material of ovine/caprine or human origin. Progress of development and use of next-generation sequencing methods was shown by several examples. Virus clearance data illustrating the effectiveness of inactivation or removal methods were presented and data provided giving insight into the mechanism of action of these technologies. In the transmissible spongiform encephalopathy (TSE) part of the conference, the epidemiology of variant Creutzfeldt-Jakob disease was reviewed and an overview about diagnostic tests provided; current thinking about the spread and propagation of prions was presented and the inactivation of prions by disinfection (equipment) and in production of bovine-derived reagents (heparin) shown. The current report provides an overview about the outcomes of the 2015 PDA Virus & TSE Safety Forum, a unique event in this field.

Evaluation of infectivity and reverse transcriptase real-time polymerase chain reaction assays for detection of xenotropic murine leukemia virus used in virus clearance validation

Infectivity and reverse transcriptase quantitative real-time polymerase chain reaction (qRT-PCR) assays have been optimized and validated for xenotropic murine leukemia virus (X-MuLV) detection. We have evaluated the assays systematically with regard to specificity, linearity, lower limit of detection (LLOD), lower limit of quantification (LLOQ), and precision. Both assays are specific for X-MuLV detection, with a linear detection range of 0.6-5.6 log(10) TCID(50)/mL for the infectivity assay, and 1.4-6.5 log(10) particles/mL for the qRT-PCR assay. The LLOD and LLOQ of the infectivity and the qRT-PCR assays are determined as 0.5 and 1.0 log(10)/mL, and 1.4 and 2.2 log(10)/mL. The inter-assay repeatability of qRT-PCR assay (4.2% coefficient of variation [CV]) is higher than the infectivity assay (7.9% CV). We have shown that both assays are closely correlated (r = 0.85, P < 0.05, n = 22). The particle/infectivity ratio is determined as 66. Both assays were applied to evaluate virus removal using virus clearance samples of chromatographic and filtration processes. Here, we have demonstrated that the qRT-PCR assay is much faster in testing and is approximately 8-fold more sensitive than the infectivity assay. Therefore, the qRT-PCR assay can replace the infectivity assay in many cases, but both assays are complementary in elucidating the mechanism of virus inactivation and removal in virus clearance validation.

Fas/FasL and perforin-granzyme pathways mediated T cell cytotoxic responses in infectious bursal disease virus infected chickens

Infectious bursal disease (IBD) is a highly contagious disease of chickens which leads to immunosuppression. In our previous study it was demonstrated that, possibly, CD4(+) and CD8(+) T cells may employ perforin and granzyme-A pathway for the clearance of IBDV-infected bursal cells. In this study, we evaluated the cytotoxic T cell responses involving two independently functioning but complementary mechanisms: Fas-Fas ligand and perforin-granzyme pathways in IBDV-infected chickens. As demonstrated previously, infection of chickens with IBDV was accompanied by influx of CD8(+) T cells in the bursa and spleen. There was an upregulation in the gene expression of cytolytic molecules: Fas and Fas ligand (FasL), perforin (PFN) and granzyme-A (Gzm-A) in bursal and in the splenic tissues of IBDV inoculated chickens. Additionally, for the first time, we detected Fas, Fas ligand, Caspase-3 and PFN producing CD8(+) T cells in the bursa and spleen of IBDV-infected chickens. The infiltration and activation of CD8(+) T cells was substantiated by the detection of Th1 cytokine, IFN-γ. These data suggest that T cells may be involved in the clearance of virus from the target organ bursa and peripheral tissues such as spleen. The findings of these studies provide new insights into the pathogenesis of IBD and provide mechanistic evidence that the cytotoxic T cells may act through both Fas-FasL and perforin-granzyme pathways in mediating the clearance of virus-infected cells.