Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 261
Filter
1.
Clinica Chimica Acta ; 530:S40-S41, 2022.
Article in English | EMBASE | ID: covidwho-1885650

ABSTRACT

Background-aim: A lesson learned already in the early phase of the COVID-19 pandemic is the need for diagnostic tools that target different biomolecules, using orthogonal experimental setups and fit-for-purpose specification of detection, in addition to the well accepted reverse transcription polymerase chain reaction (RT-PCR). Methods: The Cov-MS effort developed an isotope dilution (based on QconCAT technology) - liquid chromatography mass spectrometry (LC-MS) method that allows accurate, high throughput measurement of SARS-CoV-2 nucleocapsid (NCAP) protein. It uses Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) technology to enrich and quantify proteotypic peptides of the NCAP protein from trypsin-digested samples from COVID-19 patients. The method is for a bigger part automatable (in terms of the sample preparation, digestion, peptide enrichment and LC-MS measurements). Results: The Cov2MS assay is compatible with most matrices including nasopharyngeal swabs, saliva and blood plasma, with a sensitivity into the attomole range thanks to the peptide enrichment. The latter also reduces dependency upon LC and allows shortening of LC run time, resulting in the analysis of up to 500 samples per day per MS instrument. There is a strong positive correlation between the SISCAPA antigen assay and qPCR detection up to a Cycle threshold (Ct) of 30. Importantly, peptide enrichment allowed detection of NCAP protein in a pooled sample containing a single PCR positive patient mixed with 31 PCR negative samples, without loss in sensitivity. Finally, we also demonstrated that it is feasible to rapidly adapt the method for the incorporation of ever emerging variants of concern (VoC), and even other types of respiratory viruses (e.g. Influenza A and B). Conclusions: In conclusion, since the Cov2MS assay is insensitive to pooling and easily multiplexed, it can provide longitudinal epidemiological monitoring of large numbers of pathogens within a population and can be applied as an early warning system.

2.
BMC Infect Dis ; 22(1): 540, 2022 Jun 13.
Article in English | MEDLINE | ID: covidwho-1886923

ABSTRACT

BACKGROUND: The impact of the variant of concern (VOC) Alpha on the severity of COVID-19 has been debated. We report our analysis in France. METHODS: We conducted an exposed/unexposed cohort study with retrospective data collection, comparing patients infected by VOC Alpha to contemporaneous patients infected by historical lineages. Participants were matched on age (± 2.5 years), sex and region of hospitalization. The primary endpoint was the proportion of hospitalized participants with severe COVID-19, defined as a WHO-scale > 5 or by the need of a non-rebreather mask, occurring up to day 29 after admission. We used a logistic regression model stratified on each matched pair and accounting for factors known to be associated with the severity of the disease. RESULTS: We included 650 pairs of patients hospitalized between Jan 1, 2021, and Feb 28, 2021, in 47 hospitals. Median age was 70 years and 61.3% of participants were male. The proportion of participants with comorbidities was high in both groups (85.0% vs 90%, p = 0.004). Infection by VOC Alpha was associated with a higher odds of severe COVID-19 (41.7% vs 38.5%-aOR = 1.33 95% CI [1.03-1.72]). CONCLUSION: Infection by the VOC Alpha was associated with a higher odds of severe COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Aged , Cohort Studies , Female , Hospitalization , Humans , Male , Retrospective Studies
4.
J Infect Dis ; 2022 Apr 22.
Article in English | MEDLINE | ID: covidwho-1886443

ABSTRACT

SARS-CoV-2 Variants of Concern (VoCs) negatively impact the effectiveness of vaccines. In this study, we challenge hamsters with the Delta variant after two- or three-dose inoculations with SARS-CoV-2 vaccines constructed from stabilized prefusion spike proteins (S-2P) of Wuhan (W) and Beta (B) variants. Compared to three doses of W S-2P, two doses of W S-2P followed by a third dose of B S-2P induced the highest neutralizing antibody titer against live SARS-CoV-2 virus and enhanced neutralization of Omicron variant pseudovirus. Reduced lung live virus titer and pathology suggested that all vaccination regimens protect hamsters from SARS-CoV-2 Delta variant challenge.

5.
Sci Total Environ ; : 156724, 2022 Jun 15.
Article in English | MEDLINE | ID: covidwho-1886075

ABSTRACT

WBE has been a monitoring system that can give purposeful and inclusive real-time assessments of civic society as well as environmental health. This concept review introduces WBE as a surveillance scheme and initial warning outbreaks of contagious diseases caused by harmful SARS-CoV-2 with pandemic potential. Examining biomarkers of contagious diseases as evidence in polluted water taken from wastewater treatment plants suggests that these systems can be examined to get epidemiological data for checking the transmission of infectious B.1.1.529 to different areas. Thereafter, various benefits of surveillance are provided to analyse health information and pinpoint different problems that may be occurring in the workstation. Surveillance is followed by intervention steps that improved the work environment and prevent further progression of the disease. This information will help to improve early detection strategies, designing a prevention strategy to reduce their spread, infection control and therapies, thus, strengthening our global preparedness to fight future epidemics. In the end, a comprehensive discussion on the remaining challenges and opportunities for epidemiology has been given for future research perspectives.

7.
Immun Inflamm Dis ; 10(7): e664, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1885400

ABSTRACT

INTRODUCTION: Emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have resulted in new challenges for epidemic prevention and control worldwide. However, little is known about the latent period of coronavirus disease by the SARS-CoV-2 Delta variant of concern (VOC) in the postvaccination era. METHODS: The epidemiology and clinical data of cases with confirmed SARS-CoV-2 Delta VOC infection were retrospective collected. Dates of the first positive PCR test were collected to estimate the distribution of latent period. RESULTS: Of the 40 patients, 16 were male (40%). The median age of patients was 47.5 years. The median latent period of patients was 6.0 days (interquartile range [IQR], 4.0-9.0 days) and the longest latent period was 13.0 days after exposure. The latent periods were longer in male patients compared to female patients (median, 8.5 days vs. 5.0 days, p = .041). The median latent period was comparable among fully vaccinated cases (6.5 days), no vaccinated cases (7.5 days), and partially vaccinated cases (5.5 days). CONCLUSIONS: The median latent period of SARS-CoV-2 Delta VOC infection was 6.0 days. The latent period between vaccinated and non-vaccinated patients was not significantly different. The 14-day quarantine program is sufficient to prevent the transmission of COVID-19 by Delta VOC in the postvaccination era.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/prevention & control , Female , Humans , Male , Middle Aged , Polymerase Chain Reaction , Retrospective Studies , SARS-CoV-2/genetics
8.
Topics in Antiviral Medicine ; 30(1 SUPPL):93-94, 2022.
Article in English | EMBASE | ID: covidwho-1881051

ABSTRACT

Background: The SARS-CoV-2 pandemic has affected more than 250 million people worldwide resulting in 5 million deaths. To contain the pandemic, there is a continued need for safe vaccines that provide durable protection at low and scalable doses that easily delivered. Previously, we showed that an adeno-associated virus (AAV)-based vaccine candidate (AC1) elicited high humoral and cellular immunogenicity in mice and nonhuman primates (NHP) following a single injection, which provided near-sterilizing immunity against SARS-CoV-2 in NHP. Here, we developed optimized AAVCOVID vaccine candidates for higher potency and protection against variants of concern (VOC). Methods: The promoter in AC1 vector was substituted by three different promoters to increase the expression of Spike and they were tested in mice by single IM injection. Transgene expression and anti-Spike antibody and cellular responses were determined to assess vector potency. Then, the candidate that showed higher potency (ACM1) was engineered to express the Beta (ACM-Beta) and Delta (ACM-Delta) VOC Spike. The immunogenicity provided by ACM-Beta and ACM-Delta was characterized in mice and NHP. The cross-reactivity with the Wuhan and VOC Spikes was also assessed in the animals immunized with different Spike variants. Finally, challenge and durability studies were performed in NHPs vaccinated with the new candidates. Results: Vaccination with ACM1 candidate (miniCMV promoter) resulted in 100-fold higher Spike expression and 40-fold higher antibody responses compared to the prototypic AC1 candidate in mice. When ACM1, ACM-Beta and ACM-Delta were compared in mice, we found that the immune responses against the self-transgene were not significantly different. However, cross-reactivity was different, being ACM-Delta the candidate that better cross-neutralized the different VOC. Similar results were observed in NHP: higher potency of the candidates carrying the miniCMV promoter and similar cross-reactivity profiles. Additionally, ACM-Beta showed protection against Beta SARS-CoV-2 challenge and a durability study for ACM-Delta is ongoing. Conclusion: This work shows the adaptability and versatility of AAVCOVID vaccine platform to improve potency and protect against VOC. These observations together with the single, low dose requirement, high yield manufacturability, and 1-month stability for storage at room-temperature may make this technology well-suited to support effective immunization campaigns for emerging pathogens on a global scale.

9.
Topics in Antiviral Medicine ; 30(1 SUPPL):63, 2022.
Article in English | EMBASE | ID: covidwho-1881050

ABSTRACT

Background: During the beginning of the SARS-CoV-2 pandemic the D614G mutation in Spike protein appeared and became the first dominant variant across the globe. This mutation led to increased infectivity and stability of the spike protein and its importance is highlighted by being the one common mutation between every spike variant of concern that has come after the original. We asked how dependent spikes of subsequent lineages were on the D614G mutation and whether lineages in the absence of D614G had other mutations that increased fitness compared to the ancestral Wu-1 strain. Methods: We explore the contribution of D614G and other identified stabilizing mutations on spike mediated infectivity by incorporating them into different spike constructs. Psuedotyped lentiviral and SARS-CoV-2 virus like particle (VLP) reporters are utilized along with biochemical analysis probing expression, processing, and incorporation of spike constructs into VLPs. Results: We identify that the D614G mutation is critical for stability, infectivity, and virion loading in a number of prominent variants of concern and dominant lineages. Studying spike variants that were in circulation in absence of D614G mutation led to identification of a number of mutations at the S1 S2 interface performing similar stabilizing spike function as D614G, increasing infectivity compared to the ancestral Wu-1 Spike. The dependence on the presence of D614G or other stabilizing mutations only increased in the presence accumulating S1 mutations and specifically mutations that increase processing of spike by host furin protease, such as P681R. Conclusion: Though D614G increased stability and infectivity on the Wu-1 background, other mutations are able to perform the same role. However as more mutations accumulated in spike in the presence of D614G other stabilizing mutations are unable to fully rescue infectivity in absence of D614G, indicating a clear reliance on D614G for function. Identifying this as a critical mutation in the spike may inform future vaccine design and prediction of possible mutations that are compatible with and functional on D614G containing spike lineages.

10.
Topics in Antiviral Medicine ; 30(1 SUPPL):63, 2022.
Article in English | EMBASE | ID: covidwho-1881039

ABSTRACT

Background: SARS-CoV-2 variants of concern harbor mutations in the Spike (S) glycoprotein that confer more efficient transmission and dampen the efficacy of COVID-19 vaccines and antibody therapies. S mediates virus entry and is the primary target for antibody responses, with structural studies of soluble S variants revealing an increased propensity towards conformations accessible to the human Angiotensin-Converting Enzyme 2 (hACE2) receptor. However, real-time observations of conformational dynamics that govern the structural equilibriums of the S variants have been lacking. Methods: Here, we report single-molecule Förster Resonance Energy Transfer (smFRET) studies of S variants of concern containing critical mutations, including D614G and E484K, in the context of virus particles. Results: Investigated variants were shown by smFRET to predominantly occupy more open hACE2-accessible conformations, agreeing with predictions from structures of soluble trimers. Additionally, S variants exhibited decelerated transitions from hACE2-accessible/bound states. Conclusion: Here, we provide the real-time dimension to distinct structures of Spikes in the context of virus particles and present the first experimental evidence of increased stability of Spike variants. Our finding of increased S kinetic stability in the open conformation provides a new perspective on SARS-CoV-2 adaptation to the human population.

11.
Topics in Antiviral Medicine ; 30(1 SUPPL):101, 2022.
Article in English | EMBASE | ID: covidwho-1880973

ABSTRACT

Background: The emergence of new SARS-CoV-2 variants raises concerns whether preexisting artificial (vaccine-induced) and natural immunity from prior COVID-19 prevents re-infections. Here, we investigated the differences in primary humoral immune response following SARS-CoV-2 variants of concern (VOCs) infection and aimed to identify the key mutations involved in these differences. Methods: Patients with primary PCR-proven SARS-CoV-2 infection with no history of previous COVID-19 vaccination were included between October 2020 and May 2021 at Amsterdam UMC and via the Dutch SARS-CoV-2 sequence surveillance program. Serum was collected 4-8 weeks after symptom onset and tested for IgG binding and pseudovirus neutralization of the wild-type (WT, Wuhan/D614G), Alpha, Beta and Delta variants. Results: We included 51 COVID-19 patients, who were infected with the WT (n=20), Alpha (n=10), Beta (n=9) or Delta variant (n=12). Generally, the highest neutralization titers were against the autologous virus. After stratifying for hospitalization status, non-hospitalized patients infected with the WT (ID50 817) or Alpha (ID50 2524) variant showed the strongest geometric mean autologous neutralization, followed by the Delta variant (ID50 704) infected participants. By contrast, only one participant infected with the Beta variant showed strong autologous neutralization (median ID50 171). The VOCs also differed in their ability to induce cross-neutralizing responses, with WT-infected patients showing the broadest immune response, followed by Alpha, Delta and Beta infected participants. Additionally, participants infected with the WT, Alpha or Delta variant showed the lowest cross-neutralization against the Beta variant, with a median 5.0-fold (2 to 16-fold), 7.7-fold (2 to 32-fold), and 5.3-fold (1 to 19-fold) reduction compared to the autologous neutralization, respectively. We identified the E484K mutation as the key mutation responsible for this low cross-neutralization. Conclusion: We demonstrated that even small differences in the S protein influences the polyclonal antibody response following infection. The low level of (cross-)neutralization induced by the Beta variant may implicate a higher re-infection risk, but further research of the memory B cell compartment and clinical studies are needed. The broadest cross-neutralizing response observed for WT-infected patients suggests that artificial immunity induced by the current approved COVID-19 vaccines already protects against many re-infections.

12.
Topics in Antiviral Medicine ; 30(1 SUPPL):101-102, 2022.
Article in English | EMBASE | ID: covidwho-1880960

ABSTRACT

Background: Understanding the determinants of long-term immune responses to SARS-CoV-2 and the concurrent impact of vaccination and emerging variants of concern will guide optimal strategies to achieve global protection against the COVID-19 pandemic. Methods: A prospective cohort of 332 COVID 19 patients was followed beyond one year. Plasma neutralizing activity was evaluated using HIV-based reporter pseudoviruses expressing different SARS-CoV-2 spikes and was longitudinally analyzed using mixed-effects models. Results: Long-term neutralizing activity was stable beyond one year after infection in mild/asymptomatic and hospitalized participants. However, longitudinal models suggest that hospitalized individuals generate both short-and long-lived memory B cells, while responses of non-hospitalized were dominated by long-lived B cells. In both groups, vaccination boosted responses to natural infection. In unvaccinated participants, viral variants, mainly beta, reduced the efficacy of long-term (>300 days from infection) neutralization. Importantly, despite showing higher neutralization titers, hospitalized patients showed lower cross-neutralization of beta variant compared to non-hospitalized. Multivariate analysis identified severity of primary infection as the factor that independently determines both the magnitude and the inferior cross-neutralization activity of long-term neutralizing responses. Conclusion: Neutralizing response induced by SARS-CoV-2 is heterogeneous in magnitude but stable beyond one year after infection. Vaccination boosts these long-lasting natural neutralizing responses and should help counteract the resistance to neutralization of variants of concern such as the beta variant. Severity of primary infection determines higher magnitude but poorer quality of long-term neutralizing responses.

13.
Topics in Antiviral Medicine ; 30(1 SUPPL):91, 2022.
Article in English | EMBASE | ID: covidwho-1880937

ABSTRACT

Background: While the standard regimen of the BNT162b2 mRNA vaccine includes two doses administered three weeks apart, some public health authorities decided to space them in a context of vaccine scarcity. This decision raised concerns about vaccine efficacy, notably against the many circulating variants. In this study, we analyzed the longitudinal humoral responses from before the first dose to 4 months after the second dose in a cohort of SARS-CoV-2 naïve and previously infected (PI) individuals, with an interval of sixteen weeks between the two doses. We compared these responses to those elicited in individuals receiving the three weeks dose interval. Methods: We measured the level of antibodies recognizing SARS-CoV-2 Spike or its receptor-binding domain, and the capacity of these antibodies to neutralize several variants of concern (VOCs) and other human coronaviruses. We also measured B cell responses and Fc-mediated effector functions (ADCC) elicited by vaccination. Results: We observed that in PI individuals, the first dose led to strong humoral responses that could not be significantly improved further upon administration of a second dose. In the naïve individual's group, the first dose induced weak neutralizing activity but strong Fc-mediated functions and the administration of the second dose 16 weeks after led to a significant increase of humoral responses, achieving similar levels to those measured in PI individuals. In both groups, we observed that plasmas were able to recognize and neutralize the Spike of different VOCs but also SARS-CoV-1. Conclusion: Our results show that individuals that received the extended BNT162b2 vaccine interval developed strong humoral responses. For the naïve donors, these responses were superior to those elicited by the three-week dose interval and comparable to the PI responses after one or two doses.

14.
Topics in Antiviral Medicine ; 30(1 SUPPL):67, 2022.
Article in English | EMBASE | ID: covidwho-1880874

ABSTRACT

Background: The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with decreased susceptibility to neutralizing antibodies are of clinical importance. While several demographic and clinical correlates of Coronavirus Disease 2019 (COVID-19) outcome have been identified, their relationship to virological and immunological parameters remain poorly defined. Here, we evaluate viral diversity and the accumulation of intra-host mutations over time in a population of hospitalized adults positive for SARS-CoV-2. Methods: We performed longitudinal collection of nasopharyngeal swabs and blood samples from a small cohort of hospitalized adults with COVID-19. Clinical information regarding study subject's immunocompromised status was collected. Samples were assessed for SARS-CoV-2 viral load, viral genotype, viral diversity, and antibody titer. Results: Intra-host viral genetic diversity remained constant through disease course in study subjects that were non-immunocompromised and resulted in changes in viral genotype in some participants. We report the de novo emergence of Spike mutations that have been previously associated with circulating variants of concern in two immunosuppressed patients with persistent SARS-CoV-2 infection. Conclusion: Constant rates of viral evolution suggest the emergence of variants as a function of time, emphasizing the need for effective antivirals to control viral load over long disease courses.

15.
JMIR Public Health Surveill ; 8(6): e37377, 2022 06 03.
Article in English | MEDLINE | ID: covidwho-1881329

ABSTRACT

BACKGROUND: The Omicron variant of SARS-CoV-2 is more transmissible than prior variants of concern (VOCs). It has caused the largest outbreaks in the pandemic, with increases in mortality and hospitalizations. Early data on the spread of Omicron were captured in countries with relatively low case counts, so it was unclear how the arrival of Omicron would impact the trajectory of the pandemic in countries already experiencing high levels of community transmission of Delta. OBJECTIVE: The objective of this study is to quantify and explain the impact of Omicron on pandemic trajectories and how they differ between countries that were or were not in a Delta outbreak at the time Omicron occurred. METHODS: We used SARS-CoV-2 surveillance and genetic sequence data to classify countries into 2 groups: those that were in a Delta outbreak (defined by at least 10 novel daily transmissions per 100,000 population) when Omicron was first sequenced in the country and those that were not. We used trend analysis, survival curves, and dynamic panel regression models to compare outbreaks in the 2 groups over the period from November 1, 2021, to February 11, 2022. We summarized the outbreaks in terms of their peak rate of SARS-CoV-2 infections and the duration of time the outbreaks took to reach the peak rate. RESULTS: Countries that were already in an outbreak with predominantly Delta lineages when Omicron arrived took longer to reach their peak rate and saw greater than a twofold increase (2.04) in the average apex of the Omicron outbreak compared to countries that were not yet in an outbreak. CONCLUSIONS: These results suggest that high community transmission of Delta at the time of the first detection of Omicron was not protective, but rather preluded larger outbreaks in those countries. Outbreak status may reflect a generally susceptible population, due to overlapping factors, including climate, policy, and individual behavior. In the absence of strong mitigation measures, arrival of a new, more transmissible variant in these countries is therefore more likely to lead to larger outbreaks. Alternately, countries with enhanced surveillance programs and incentives may be more likely to both exist in an outbreak status and detect more cases during an outbreak, resulting in a spurious relationship. Either way, these data argue against herd immunity mitigating future outbreaks with variants that have undergone significant antigenic shifts.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Disease Outbreaks , Humans , Pandemics , Public Health Surveillance/methods
16.
Topics in Antiviral Medicine ; 30(1 SUPPL):63-64, 2022.
Article in English | EMBASE | ID: covidwho-1880680

ABSTRACT

Background: Humoral innate immunity consists of a limited, but diverse, set of humoral fluid phase pattern recognition molecules (PRMs) that represent a first line of resistance against microbial invaders by promoting pathogen disposal by phagocytosis, complement activation and inflammation. These factors encompass complement, ficolin, collectin and pentraxin family of proteins. Methods: We have analyzed the activity of PRMs for their potential capacity of inhibiting SARS-CoV-2 entry and replication into epithelial cells by a microneutralization assay based on a lentiviral particles pseudotyped with the SARS-CoV-2 spike protein in HEK293T cells overexpressing the angiotensin converting enzyme 2 (ACE2). Either SARS-CoV-2 or target cells were incubated with Mannose Binding Lectin (MBL, concentration range: 1-50 μ g/ml) to further characterize its anti-viral activity for 1 h prior to infection in both human Calu-3 cells and air-liquid interface cultures of human bronchial epithelial cells (HBEC). Binding experiments were carried out with SARS-CoV-2 Spike protein and recombinant MBL to further investigate its antiviral action. Results: Among 12 PRMs tested, only MBL inhibited viral entry in the pseudotyped neutralization assay. Furthermore, MBL protein inhibited SARS-CoV-2 viral replication in Calu-3 and HBEC by ca. one log10 at the top concentration (10 μ g/ml and 50 μ g/ml, respectively). MBL antiviral activity was confirmed also against alpha, beta and gamma SARS-CoV-2 variants of concern. Binding experiments showed that MBL specifically interacts with the trimeric form of SARS-CoV-2 spike. Conclusion: MBL binds to the Spike protein in its active trimeric conformation leading to the inhibition of SARS-CoV-2 infection and replication in vitro. These results suggest that MBL possesses an antiviral activity against SARS-CoV-2 that could bear therapeutic potential.

17.
Topics in Antiviral Medicine ; 30(1 SUPPL):176, 2022.
Article in English | EMBASE | ID: covidwho-1880565

ABSTRACT

Background: Few data are available about comparison of different monoclonal antibodies (MAbs) for COVID-19 in the real-world setting. We aim to compare effectiveness of bamlanivimab/etesevimab (BAM/ETE) versus (vs) casirivimab/imdevimab (CAS/IMD) and to estimate predictors of hospitalization/death. Methods: Observational analysis of all consecutive outpatients (pts) with mild/moderate COVID-19 enrolled within the AIFA access program in a single center in Rome, from March to October, 2021. At first baseline (BL) visit, RT-PCR from nasopharyngeal swab with cycle thereshold (CT) measurement and viral sequencing was performed. Pts received intravenous BAM/ETE (700/1400 mg) or CAS/IMD (1200/1200 mg) and were followed through day 30. Primary endpoint was hospitalization/death due to severe COVID-19 by day 30. Average treatment effect (ATE) in the multiplicative scale of the odds was the chosen estimand to compare the two treatments, adjusted for age, obesity, time from onset to infusion, median C-reactive protein (CRP), vaccination, variant of concern (VOC) and BL-CT. Predictors of clinical failure were explored by two different models of multivariable logistic regression. Results: 242 pts receiving BAM/ETE (n=76) or CAS/IMD (n=166) were included (male 54%;median age 65 yrs;median SpO2 97%;diabetes 12%;hypertension 40%;CVD 17%;COPD 26%;autoimmune diseases 12%;immunodeficiency 18%). Median time from symptoms onset to infusion was 4 days (IQR 3-6). No differences were observed between the two MAbs for BL characteristics except for BMI>35 (BAM/ETE 24%, CAS/IMD 12%), CRP (BAM/ETE 1.8, CAS/IMD 1.2), vaccination (BAM/ETE 26%, CAS/IMD 46%) and distribution of VOC (Alpha 46% BAM/ETE vs 22% CAS/IMD;Gamma 20% vs 7%;Delta 5% vs 55%). Proportion of patients with COVID-related hospitalization/death by day 30 was 12/76 (15.8%) for BAM/ETE and 6/166 (3.6%) for CAS/IMD. Estimate of causal effect of BAM/ETE exposure compared to CAS/IMD on primary end point by ATE is reported in Table 1a. Factors associated with an increased risk of clinical failure by fitting multivariable logistic regression were BMI >35 and P1/Gamma VOC;higher BL-CT was associated with a reduced risk (Table 1b-1c). Conclusion: In a real-life setting, receiving BAM/ETE was associated with a 4-fold higher risk of COVID-19 progression to hospitalization/death than CAS/IMD. SARS-CoV-2 P.1/Gamma, but not B.1617.2/Delta VOC, obesity and higher BL viral load also predicted an increased risk of clinical worsening.

18.
Topics in Antiviral Medicine ; 30(1 SUPPL):121, 2022.
Article in English | EMBASE | ID: covidwho-1880494

ABSTRACT

Background: Identifying Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) specific T-cell epitope-derived peptides that are also found within variants of concern (VOC) is critical for measuring the duration of cellular immunity induced by the virus and COVID-19 vaccines. Therefore, we assessed whether the peptides selected from topologically important regions of SARS-CoV-2 proteins avoid major mutations of VOC and induce T-cell immune response. Methods: We selected 32 peptides within topologically important regions of SARS-CoV-2 Spike (S) and Nucleocapsid (NC) proteins by applying an insilico pipeline to 607 viral sequences in 2019. To determine if these peptides avoid VOC mutations, we analyzed S and NC protein regions derived from 1.7 x 106 viral genomic sequences compiled from Mar 2020-Aug 2021. We identified α-, β-and δ-VOC mutations found within >1% of the S and NC protein sequences. These mutations were compared to the peptides. To determine T-cell immune response to these selected peptides as a pool, we assessed interferon-γ (IFN-γ), interleukin-2 (IL-2), tumor necrosis factor-α (TNF-α) and CD107a/b (degranulation marker) production within peripheral blood mononuclear cell (PBMC) samples derived from COVID-19 post-recovery donors (n=23) by employing dual color FluoroSpot and intracellular cytokine staining (ICS). Results: We found 88% of S protein-derived peptides did not contain mutations of α-, β-and δ-VOC. All peptides from S protein (n=25) avoided known T-cell escape mutations. Of the 7 NC-derived peptides, three contained the L139F mutation found within α-and δ-VOC, however, this mutation was observed within <2% NC protein sequences. A peptide pool containing our 32 selected peptides elicited an immune response within PBMCs from 17/23 COVID-19 post-recovery donors. FluoroSpot analysis revealed IFN-γ and IL-2 production to our peptide pool was similar/higher compared to the commercial S and NC peptide pools. The response of CD4 and CD8 T-cells to our peptide pool was polyfunctional expressing ≥2 markers within most of the donors when ICS was performed, with IFN-γ and TNF-α being the main cytokines produced. Conclusion: Applying an immunoinformatics pipeline allowed us to select peptides from the S and NC proteins which avoid the majority of mutations found within the α-, β-and δ-VOC. Our peptide pool elicited a polyfunctional T-cell response making it an ideal candidate for assessing the duration of cellular immunity induced by SARS-CoV-2 variants and vaccines.

19.
Topics in Antiviral Medicine ; 30(1 SUPPL):117, 2022.
Article in English | EMBASE | ID: covidwho-1880460

ABSTRACT

Background: The innate immune system is a powerful anti-viral defense mechanism, which includes the interferon (IFN) system and autophagy. Thus, successful pathogens like SARS-CoV-2 need to counteract or evade these defenses to establish an infection. However, due to its ongoing, worldwide spread in the human population SARS-CoV-2 is evolving and in the meantime four variants with selection advantages (variants of concern) emerged. Methods: Using expression constructs for 29 SARS-CoV-2 proteins we evaluated the impact of individual viral proteins on induction of cytokines (IFNA4, IFNB1, IRF3-signalling, NF-κB-signaling) and cytokine signaling (IFNα2, IFNβ, IFNγ, IFNa;1, IL-1α, TNFα) in luciferase reporter assays, validated by endogenous transcription factor phosphorylation analysis. We assessed the influence of SARS-CoV-2 proteins on autophagy using a flow cytometry-based system. Underlying molecular mechanisms were investigated on an endogenous level using Western blot, confocal fluorescence microscopy, and flow cytometry. In addition, we examined the susceptibility of SARS-CoV-2 including all variants of concern towards type-I,-II, and-III interferons. Results: To understand how SARS-CoV-2 efficiently manipulates the host's innate immune defenses, we systematically analyzed the impact of SARS-CoV-2 encoded proteins on induction of various IFNs and pro-inflammatory cytokines, IFN signaling, and autophagy. Our results reveal the range of innate immune antagonists encoded by SARS-CoV-2 and we characterized selected molecular mechanisms employed by Nsp1 and Nsp14 to downregulate the IFN system or ORF3a and ORF7a to prevent autophagic degradation. Interestingly, our assays show that variants of concern of SARS-CoV-2 remain sensitive to type-II interferon signaling but show increased resistance towards type-I and/or type-III interferons. Conclusion: SARS-CoV-2 has evolved to counteract innate immunity using several synergistic approaches but remains relatively sensitive to type-II and-III interferons. However, emerged variants of concern remain sensitive overall but are less susceptible towards IFNα2/β and IFNa;1 than early SARS-CoV-2 isolates.

20.
Topics in Antiviral Medicine ; 30(1 SUPPL):102, 2022.
Article in English | EMBASE | ID: covidwho-1880437

ABSTRACT

Background: Although presence of SARS-CoV-2 neutralising antibodies can provide protection against development of COVID-19, how reflective circulating anti-SARS-CoV-2 antibody levels are of underlying neutralising capacity, and whether a threshold exists to predict sufficient neutralising capacity remains unclear. Methods: In plasma from individuals with PCR-confirmed COVID-19 recruited to the All Ireland Infectious Diseases Cohort Study, we measured IgG concentrations against RBD, Spike protein sub-unit 1 and 2 (S1, S2) and Nucleocapsid (NC) using multiplex electrochemiluminescence (normalised to World Health Organisation reference serum as IU/mL). Neutralising capacity was measured against live SARS-CoV-2 virus (clinical isolate 2019-nCoV/Italy-INMI1) by determining the maximum plasma dilution required to maintain 50% inhibition of infection of Vero E6 cells (50% Neutralisation Titre (NT50)), by flow cytometry-based micro-neutralisation assay. Given that the Beta SARS-CoV-2 variant of concern (VOC) reduces neutralising activity up to six fold, we estimated a NT50 of 1:1000 against wild type SARS-CoV-2 would maintain neutralising activity against VOC. We used Spearman correlation and linear regression to model relationships between NT50 and IgG concentrations. Data are presented as median (IQR) unless specified. Results: In 190 individuals (age 50 (40-64) years, 55% female, time from symptom onset 98 (35-179) days), NT50 most highly correlated with anti-RBD IgG (Rho 0.81 p<0.001, Fig 1a) compared with other IgG classes (S1;Rho 0.8, S2;0.73, NC;0.72, all p<0.001). Median RBD titre was 246 (71-662) but trended lower over time, with a median of 319 (61-1012) IU/ml at 0-90 days, 244 (86-523) IU/ml at 90-180 days and 157 (80-364) IU/ml at >180 days post symptom onset respectively (p=0.08, Fig 1b). RBD IgG titres of 476 IU/ml corresponded to a NT50 of 1:1000. Overall, RBD ≥476 IU/ml predicted NT50 ≥1:1000 with a sensitivity of 77 (95% CI 65-87)% and specificity 89 (95% CI 82-93)%. This improved in an analysis restricted to convalescent samples (>30 days post symptom onset, n=148), with a sensitivity 88% (95% CI 74-96%) and specificity 90% (95%CI 82-95%) respectively. Conclusion: In convalescent plasma, RBD IgG titres ≥476IU/mL is sensitive and specific for predicting robust underlying neutralising capacity. Further research is required to validate these findings in other cohorts and confirm these thresholds in post-vaccinated individuals.

SELECTION OF CITATIONS
SEARCH DETAIL