Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses

Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40x improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher Apex system.

Immunogenicity of The BNT162b2 mRNA COVID-19 Vaccine in Patients With Primary Brain Tumors: A Prospective Cohort Study

Purpose Immunogenicity of Covid-19 vaccines may be negatively impacted by anti-cancer treatment. The management of primary brain tumor (PBT) patients routinely includes temozolomide and steroids, which are immune-suppressive. In this study, we aimed to determine the rate of seropositivity in PBT patients following receipt of two doses of the BNT162b2 vaccine. Methods We prospectively evaluated IgG antibody levels against SARS-CoV-2 spike protein in 17 PBT patients following two doses of the BNT162b2 mRNA vaccine. IgG levels were collected at two time points: T1 - after a median of 44 days from the second vaccine dose and T2 - after a median of 130 days from the second dose. Titers were compared against a group of healthy controls (HC) comprised of patients’ family members/caregivers. Results At T1, 88.2% (15/17) of PBT patients achieved seroconversion, compared with 100% (12/12) of HCs. Median IgG titer was significantly lower in the PBT group compared to the HC group (1,908 AU/mL vs 8,198 AU/mL, respectively; p=0.002). At T2, 80% (12/15) of PBT achieved seroconversion, compared to 100% (10/10) of the HCs. Median IgG titer remained significantly lower in the PBT group (410 vs 1687; p=0.002). All three PBT patients who failed to seroconvert at T2 had been treated with corticosteroids during vaccination. In a univariate analysis, steroid use was negatively associated with antibody titer. Conclusion Most PBT patients achieve seroconversion after receiving the BNT162b2 vaccine, but with lower IgG titer compared to HCs. Steroid use during the vaccination period is associated with lower titer.

Seroresponse to SARS-CoV-2 vaccines among maintenance dialysis patients over six months

Background and Objectives: While most maintenance dialysis patients exhibit initial seroresponse to vaccination, concerns remain regarding the durability of this antibody response. This study evaluated immunity over time. Design, setting, participants, and measurements: This retrospective cohort study included maintenance dialysis patients from a midsize national dialysis provider who received a complete SARS-CoV-2 vaccine series and had at least one antibody titer checked after full vaccination. Immunoglobulin G spike antibodies (SAb-IgG) titers were assessed monthly with routine labs beginning after full vaccination and followed over time; the semiquantitative SAb-IgG titer reported a range between 0 and ≥20 U/L. Descriptive analyses compared trends over time by prior history of COVID-19 and type of vaccine received. Time-to-event analyses were conducted for the outcome of loss of seroresponse (SAb-IgG < 1 U/L or development of COVID-19). Cox proportional hazards regression was used to adjust for additional clinical characteristics of interest. Results: Among 1898 maintenance dialysis patients, 1567 (84%) had no prior history of COVID-19. Patients without a history of COVID-19 had declining titers over time. Among 441 BNT162b2/Pfizer recipients, median [IQR] SAb-IgG titer declined from 20 [5.99-20] U/L in month 1 to 1.30 [0.15-3.59] U/L by month 6. Among 779 mRNA-1273/Moderna recipients, median [IQR] SAb-IgG titer declined from 20 [20-20] in month 1 to 6.20 [1.74-20] by month 6. The 347 Ad26.COV2.S/Janssen recipients had a lower titer response than mRNA vaccine recipients over all time periods. In time-to-event analyses, Ad26.COV2.S/Janssen and mRNA-1273/Moderna recipients had the shortest and longest time to loss of seroresponse, respectively. The maximum titer reached in the first two months after full vaccination was predictive of the durability of the SAb-IgG seroresponse; patients with SAb-IgG titer 1-19.99 U/L were more likely to have loss of seroresponse compared to patients with SAb-IgG titer ≥20 U/L (HR 23.9 [95% CI: 16.1-35.5]). Conclusions: Vaccine-induced seroresponse wanes over time among maintenance dialysis patients across vaccine types. Early titers after full vaccination predict the durability of seroresponse.

Drug-free nasal spray as a barrier against SARS-CoV-2 infection: safety and efficacy in human nasal airway epithelia

Background: For SARS-CoV-2 and other respiratory viruses, the nasal epithelium is a key portal for infection. Therefore, the nose is an important target of prophylactic and therapeutic interventions against these viruses. We developed a nasal spray (AM-301, a medical device marketed as Bentrio) to protect against infection by SARS-CoV-2 and potentially other viruses. Aims of the study: To test the safety and efficacy of AM-301 against SARS-CoV-2 infection. Methods: AM-301 was tested on an in vitro 3D model of primary human nasal airway epithelium. Safety was assessed in assays for tight junction integrity, cytotoxicity and cilia beating frequency. Efficacy against SARS-CoV-2 infection was evaluated in prophylaxis and infection mitigation assays. Results: AM-301 did not have any detrimental effect on the nasal epithelium. Prophylactic treatment with AM-301 reduced viral titer significantly vs. controls over 4 days, reaching a maximum reduction of 99%. When treatment with AM-301 was started 24 or 30 h after infection, epithelia that received the formulation had a 12- or 14-fold lower titer than controls. Conclusion: AM-301 was found to be safe in vitro, and it significantly decelerated viral titer growth in experimental models of prophylaxis and mitigation. Its physical (non-pharmaceutical) mechanism of action, safety and efficacy pave the way for further investigation of its possible use against a broad spectrum of viruses, allergens and pollutants.

Amelioration of Beta Interferon Inhibition by NS4B Contributes to Attenuating Tembusu Virus Virulence in Ducks

Our previous studies reported that duck Tembusu virus nonstructural protein 2A (NS2A) is a major inhibitor of the IFNβ signaling pathway through competitively binding to STING with TBK1, leading to a reduction in TBK1 phosphorylation. Duck TMUV NS2B3 could cleave and bind STING to subvert the IFNβ signaling pathway. Here, we found that overexpression of duck TMUV NS4B could compete with TBK1 in binding to STING, reducing TBK1 phosphorylation and inhibiting the IFNβ signaling pathway by using the Dual-Glo® Luciferase Assay System and the NanoBiT protein-protein interaction (PPI) assay. We further identified the E2, M3, G4, W5, K10 and D34 residues in NS4B that were important for its interaction with STING and its inhibition of IFNβ induction, which were subsequently introduced into a duck TMUV replicon and an infectious cDNA clone. We found that the NS4B M3A mutant enhanced RNA replication and exhibited significantly higher titer levels than WT at 48-72 hpi but significantly decreased mortality (80%) in duck embryos compared to WT (100%); the NS4B G4A and R36A mutants slightly reduced RNA replication but exhibited the same titer levels as WT. However, the NS4B R36A mutant did not attenuate the virulence in duck embryos, whereas the G4A mutant significantly decreased the mortality (70%) of duck embryos. In addition, the NS4B W5A mutant did not affect viral replication, whereas the D34A mutant slightly reduced RNA replication, and both mutants exhibited significantly lower titer levels than the WT and significantly decreased mortality (90% and 70%, respectively) in duck embryos. Hence, our findings provide new insight into the development of attenuated flaviviruses by targeting the disabling viral strategies used to evade the innate defense mechanisms.

Optic neuritis of MOG-IgG-associated autoimmune disorders: a case report

Background The diagnosis of immunoglobulin G serum antibodies to myelin oligodendrocyte glycoprotein (MOG-IgG) associated inflammatory demyelinating disorders can be confirmed by the presence of MOG-IgG, yet its general cut-off concentration had not yet to be defined. Whether it is significant that a seropositive lower titer level for MOG-IgG could cause disease is still unknown. Case presentation A 55-year-old Chinese woman presented with acute optic neuritis manifestations in the left eye. MRI showed a left optic nerve demyelination image and a T2 hyperintensity at C7 vertebral segment without any extra specific lesions. AQP4-IgG was tested seronegative, while the MOG-IgG was positive, titer 1:10, by indirect immunofluorescence. Considering the lower concentration, we retested serum MOG-IgG after 6 months of steroid therapy, using cell-based assay, then we still got the same result which was also barely above the negative cut-off value. So, the clinical diagnose was “possible MOG-IgG-associated encephalomyelitis”. The woman’s condition improved by steroid therapy without relapse. Conclusions Seropositive MOG-IgG, even at a lower level, could lead to an autoimmune inflammatory demyelination. In adults, it commonly presents as ON and myelitis. Although the patient had a considerable reaction, steroid therapy could not make MOG-IgG seronegative, instead, the antibody may persist even during remission and flare-ups can recur after steroid withdrawal. Therefore, a long-term follow-up is necessary to monitor the patient’s prognosis.

Use of convalescent serum reduces severity of COVID-19 in nonhuman primates

Passive transfer of convalescent plasma or serum is a time-honored strategy for treating infectious diseases. Human convalescent plasma containing antibodies against SARS-CoV-2 is currently being used to treat COVID-19 patients. However, most patients have been treated outside of randomized clinical trials making it difficult to determine the efficacy of this approach. Here, we assessed the efficacy of convalescent sera in a newly developed African green monkey model of COVID-19. Groups of SARS-CoV-2-infected animals were treated with pooled convalescent sera containing either high or low to moderate anti-SARS-CoV-2 neutralizing antibody titers. Differences in viral load and disease pathology were minimal between monkeys that received the lower titer convalescent sera and untreated controls. However, and importantly, lower levels of SARS-CoV-2 in respiratory compartments, reduced gross and histopathological lesion severity in the lungs, and reductions in several parameters associated with coagulation and inflammatory processes were observed in monkeys that received convalescent sera versus untreated controls. Our data support human studies suggesting that convalescent plasma therapy is an effective strategy if donors with high level of antibodies against SARS-CoV-2 are employed and if recipients are at an early stage of disease.

Distinctive features of positive anti-cell antibody tests (indirect immunofluorescence on HEp-2 cells) in patients with non-autoimmune diseases

Objective The objective of this study was to determine whether characteristics of positive results in the indirect immunofluorescence assay on HEp-2 cells for anti-cell antibodies (HEp-2 IFA) differ between patients with non-autoimmune diseases (NADs) and patients with systemic autoimmune rheumatic diseases (SARDs). Methods Cross-sectional observational study comparing HEp-2 IFA test results in three groups: (a) 558 NAD patients comprising four subgroups (cancer ( n = 95), infectious diseases ( n = 148), psychiatric diseases ( n = 163), common non-infectious chronic diseases ( n = 152)); (b) 194 SARD patients; (c) 1217 healthy individuals (HIs). Sera were tested at 1:80 dilution and diluted to the end titer. Slides were analyzed by two independent blinded examiners. Results A positive HEp-2 IFA test occurred in 102 (18.3%) NAD patients, 170 (87.6%) SARD patients and 150 (12.3%) HIs. The four NAD subgroups did not differ regarding HEp-2 IFA frequency, titer or pattern. HEp-2 IFA titer was higher in NAD patients than in HIs and both had lower titer than SARD patients. Nuclear dense fine speckled pattern was more frequent in NAD patients and HIs than in SARD patients ( p < 0.001). Nuclear homogeneous and nuclear coarse speckled patterns were more frequent in SARD patients than in the other groups ( p < 0.001). The nuclear fine speckled pattern was prevalent in all three groups, but presented a gradient in titer across them; HIs and NAD patients had low and intermediary titers, which were significantly lower than in SARD patients ( p < 0.001). Conclusion Positive HEp-2 IFA frequency, pattern and titer present differential features in NAD and SARD patients, and this attribute adds value to the test in the diagnosis of SARDs.

Evaluation of Sb-1 bacteriophage activity in enhancing antibiotic efficacy against biofilm, degrading the exopolysaccharide matrix and targeting persister cells of Staphylococcus aureus

Most research on phage therapy focused on planktonic bacteria, whereas bacteriophage activity against biofilms is limited. We evaluated the capability of Staphylococcus aureus-specific bacteriophage Sb-1 to eradicate biofilm alone and in combination with different classes of antibiotics, to degrade the extracellular matrix and target persister cells. Biofilm of methicillin-resistant S. aureus (MRSA) ATCC 43300 was treated with Sb-1 alone or in (simultaneous or staggered) combination with either fosfomycin, rifampin, vancomycin, daptomycin or ciprofloxacin. The matrix was visualized by confocal fluorescent microscopy. Persister cells were treated with 104 and 107 PFU/mL Sb-1 for 3 hours in PBS, followed by CFU counting. Alternatively, bacteria were washed and incubated in fresh BHI medium and the bacterial growth assessed after further 24-hours. Pre-treatment with Sb-1 followed by the administration of sub-inhibitory concentrations of antibiotic exerted a considerable synergistic effect in eradicating MRSA biofilm. Sb-1 determined a dose-dependent reduction of matrix exopolysaccharide. 107 PFU/mL Sb-1 showed direct killing activity on persisters. However, even a lower titer had lytic activity when phage-treated persister cells were inoculated in fresh medium, reverting to a normal-growing phenotype. This study provides valuable data regarding the capability of Sb-1 to enhance antibiotic efficacy, exhibiting specific antibiofilm features. Its ability to degrade the MRSA polysaccharide matrix and target persister cells makes Sb-1 suitable for the therapy of biofilm-associated infections.

Physiologic, Anatomic, and Gene Expression Changes in Citrus sunki, Poncirus trifoliata, and Their Hybrids After ‘Candidatus Liberibacter asiaticus’ Infection

Huanglongbing (HLB) is a destructive disease of citrus caused by phloem-limited bacteria, namely ‘Candidatus Liberibacter asiaticus’ (Las), ‘Candidatus Liberibacter africanus’, and ‘Candidatus Liberibacter americanus’. Although there are no known HLB-resistant citrus species, studies have reported Poncirus trifoliata as being more tolerant. Assuming that callose deposition in the phloem of infected plants can inhibit translocation of photosynthetic products and cause starch accumulation, we compared callose deposition in petioles and starch accumulation in infected leaves of three genotypes (Citrus sinensis, C. sunki, and P. trifoliata) and 15 hybrids (C. sunki × P. trifoliata). Compared with the mock-inoculated plants, higher bacterial counts and greater accumulation of callose and starch were found in C. sinensis, C. sunki, and 10 of the hybrid plants. Lower titer and fewer metabolic changes due to Las infection were observed in P. trifoliata and in two Las-positive hybrids while three hybrids were Las-negative. Callose accumulation was linked to and correlated with genes involved in phloem functionality and starch accumulation was linked to up-regulation of genes involved in starch biosynthesis and repression of those related to starch breakdown. Lower expression of genes involved in phloem functionality in resistant and tolerant plants can partially explain the absence of distinct disease symptoms associated with starch accumulation that are usually observed in HLB-susceptible genotypes.