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In order to improve the detection and rapid diagnosis of the SARS-CoV-2 coronavirus, we evaluated the ID NOW™ COVID-19 isothermal gene amplification technique in parallel with the real-time PCR technique (Diasorin) routinely used in the laboratory during a prospective study in the 2020 season. As this technique showed satisfactory sensitivity and specificity of 98% and 97.5% respectively, we then proposed to implement the detection of SARS-CoV-2 coronavirus in the emergency department and maternity as a point-of-care test (POCT) for the 2020-2021 season and to evaluate its clinical and organizational impact. This article summarizes the results obtained and highlights the advantages and limitations of this strategy implemented in the emergency department, particularly in terms of time spent in the department, hospitalization rates, anticoagulant treatment and early isolation of patients, as well as the organizational impact on the maternity unit. Based on this experience, we report on the regulatory constraints that apply when setting up a POCT and the steps required to validate the accreditation in accordance with standard NF EN ISO 22870.

Objective.: To identify the presence of the SARS-CoV-2 virus in wastewater from hospitals in Peru., Materials and Methods.: Water samples were collected from the effluents of nine hospitals in Peru during March and September 2022. SARS-CoV-2 was identified by using Illumina sequencing. Variant, lineage and clade assignments were carried out using the Illumina and Nextclado tools. We verified whether the SARS-CoV-2 variants obtained from wastewater were similar to those reported by the National Institute of Health of Peru from patients during the same period and region., Results.: Eighteen of the 20 hospital wastewater samples (90%) provided sequences of sufficient quality to be classified as the Omicron variant according to the WHO classification. Among them, six (30%) were assigned by Nextclade to clades 21K lineage BA.1.1 (n=1), 21L lineage BA.2 (n=2), and 22B lineages BA.5.1 (n=2) and BA .5.5 (n=1)., Conclusions.: SARS-CoV-2 variants were found in hospital wastewater samples and were similar to those reported by the surveillance system in patients during the same weeks and geographic areas. Wastewater monitoring could provide information on the environmental and temporal variation of viruses such as SARS-CoV-2., Motivation for the study. To contribute to the surveillance of environmental samples from hospital effluents in order to achieve early warning of possible infectious disease outbreaks. Main findings. The Omicron variant of the COVID-19 virus was detected in wastewater from hospitals in Puno, Cuzco and Cajamarca; these results are similar to the reports by the Peruvian National Institute of Health based on nasopharyngeal swab samples. Implications. The presence of the Omicron variant in hospital wastewater during the third wave of the pandemic should raise awareness of the treatment system before wastewater is discharged into the public sewer system.

Background: Since the beginning of the corona pandemic in Germany in January 2020, day care centres (DCC) have faced the challenge of reliably detecting cases of SARS-CoV-2 infection as early and reliably as possible in order to avoid major outbreaks and closures. Conducting regular virological screening tests for asymptomatic DCC children and childcare workers requires a high level of acceptance among participants and should be as easy as possible to implement. The present study aimed to evaluate childcare workers' and parents' attitudes and experiences regarding the acceptance and feasibility of various screening methods. This assessment was conducted using additional qualitative interviews designed for home-based screening in the context of a screening study in DCCs., Method: From May to July 2021, childcare workers and parents of children in nine DCCs in Wuerzburg independently carried out screening tests for SARS-CoV-2 at home twice a week as part of the "Würzburg Child Care Study in the COVID-19 Pandemic 2.0". The participants were offered two self-sampling methods (mouth-rinsing fluid for pooled PCR tests and/or nasal rapid antigen self-tests). Before and after the 12-week test phase, telephone interviews were conducted with a selected sample of childcare workers and parents in order to ascertain initial attitudes and further experiences with the two self-sampling methods and their implementation. The interviews were fully transcribed for analysis and subjected to a qualitative content analysis according to Kuckartz., Results: Of the 1,026 eligible participants, 591 individuals, including 139 childcare workers and the parents of 452 children, agreed to take part in the screening tests. A total of 49 interviews were conducted with a specifically selected sample (20 before the start of the test, 29 after the end of the test). In the qualitative content analysis, three overarching topics emerged: 'aspects of the test performance', 'aspects of the perception of safety' and 'aspects of the testing in children'. Regardless of the fact that the various test methods and test features were perceived very differently, conducting the tests at home was found to be feasible., Discussion: The differentiated insights into the participants' perspectives provide valuable information about factors that influence the acceptance of self-testing. These should be taken into account before such a measure is introduced in DCCs if necessary., Conclusion: The assessment of test procedures is strongly influenced by individual preferences. Test concepts should be implemented with as little time and organisational effort as possible in order to promote willingness to participate. Clear study information and quick feedback on test results can enhance the sense of security among parents and childcare workers., (Copyright © 2024. Published by Elsevier GmbH.)

The present study assessed the diagnostic performance of the Xpert®Xpress SARS-CoV-2 test in comparison with the Charité protocol real-time RT PCR for the detection of SARS-CoV-2 in Peruvian patients. This was a diagnostic test study that included 100 nasal and pharyngeal swab samples. We obtained an overall concordance of 98.70% (95%CI: 92.98-99.97), with a kappa coefficient of 0.97 (95%CI: 0.86-1.00) and sensitivity and relative specificity rates of 100% and 96.15%, respectively. Additionally, the percentage of the area under the ROC curve was 98.08% in both cases, and an analytical specificity rate of 100% was obtained for the different respiratory viruses evaluated. In conclusion, the Xpert®Xpress SARS-CoV-2 test, by using nasal and pharyngeal swab samples, was highly sensitive and specific, and the kappa coefficient showed an excellent correlation when compared to the reference test. Motivation for the study. To describe and evaluate a closed molecular platform, easy to use and of importance in Peru for the management of diseases of public health priority, now implemented for the detection of SARS-CoV-2. Main findings. Highly sensitive and specific molecular test, with excellent correlation compared to the reference test for detecting SARS-CoV-2. Implications. Can be used in point-of-care laboratories for rapid molecular detection of different infectious agents, including SARS-CoV-2. Little expertise and minimal infrastructure are required to implement it.

Refugees and migrants remain one of the most vulnerable people and the COVID-19 pandemic has posed additional challenges both in terms of increased risk of infection and death experienced, highlighting existing inequities in access to and utilization of health services, as underlined by World Health Organization in 2020 in the Health and Migration Programme. In the context of the Programme 'Epidemiological surveillance and control of COVID-19 in metropolitan urban areas and for the containment of the circulation of SARS-CoV-2 in the migrant population in Italy', coordinated by the Italian Centre for Disease Control and Prevention (CCM) and funded by the Italian Ministry of Health, an experimental epidemiological, virological, and molecular SARS-CoV-2 surveillance system addressed to migrant populations in Sicily through Mediterranean routes was implemented. To this end, a multidisciplinary network supported by a hub&spoke system of laboratories was established in Sicily Region (Southern Italy), using molecular and Next Generation Sequencing (NGS) techniques to identify different SARS-CoV-2 strains in relation to migration flows. Herein, the lesson learnt through this integrated surveillance model, that was in place from February 2021 till the end of the COVID-19 emergency in Italy, are reported. Overall, the data emphasized the need for enhancing molecular surveillance in the areas of the globe where testing and sequencing resources are limited. The epidemiological, virological, and molecular SARS-CoV-2 monitoring, targeted to the migrant population, may also provide a valuable experimental model.

Voluntary associations played a decisive role during the SARS-CoV-2 pandemic. This contribution reports on the experience of the Torino Street Care project, whose members carried out swabs in informal facilities, visits, drug distribution, reading examinations, and orientation interviews. They also provided social, legal, or bureaucratic help, distributed food and collaborated in the vaccination campaign. These activities enabled a relationship of trust to be created with the migrant population in the Piedmont Region (Northern Italy), also thanks to the clarity and the precision of the communication the volunteers had with the people they welcomed.

Polymerase chain reaction (PCR) and antigen test (AgT) are frequently used in the diagnosis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Routine PCR tests that detect the virus genome cannot determine whether the virus is infectious or not. However, detection of subgenomic RNA (sgRNA) produced during the replication period may indicate active viral infection. Active virus detection can offer various health and economic benefits from isolation time to treatment. Antigen tests are also considered as indicators of infectiousness since they can detect viruses above a certain load amount. The aim of this study was to use two different subgenomic RNAs and antigen test instead of genomic RNA to examine the relationship with each other and the clinic in terms of infectiousness. Evaluating the antigen test together with subgenomic RNA as an indicator of infectiousness may show the importance of this test. SARS-CoV-2 PCR positive 109 naso/oropharyngeal swab samples stored at -80 °C were included in the study. In order to confirm the PCR positivity of these samples, E gene PCR was performed and AgT, and E and N sgRNA quantitative real-time reverse transcription-PCR (RT-qPCR) detection was performed. Of the 109 SARSCoV-2 PCR positive samples, 83 (76.14%) had antigen test positivity, 88 (80.73%) had E gene sgRNA, 96 (88.07%) had N gene sgRNA and 97 (89%) had at least one sgRNA positivity.The antigen test was found positive in 77.3% of the samples in which at least one sgRNA was detected and in 66.7% of the negative samples and this difference was not statistically significant (p= 0.475). The difference between E sgRNA and AgT positivity was significant (p= 0.023). N sgRNA was positive in 98.9% of E sgRNA positive samples and 42.9% of the negative samples and this difference was statistically significant (p= 0.0001). The AgT positivity rate was found to be 98.15% (53/54) for cycle threshold (Ct) value ≤ 25, 57.14% (12/21) for Ct 25-30, and 52.94% (18/34) for Ct ≥ 30. The difference in antigen test positivity between E gRNA Ct value ≤ 25 and > 25, ≤ 29 and > 29, < 30 and ≥ 30 was statistically significant (p= 0.0001). Antigen test positivity appears to be associated with viral load and infectivity, as expected. In our study, it has been shown that sgRNAs and AgT which are indicators of infectiousness can be detected at least 10 days after the symptom period. Using these two tests together could detect infective individuals with higher accuracy and shorten the duration of hospital stay and isolation.

Objective: To determine the seroprevalence of SARS-CoV-2 in patients with immune-mediated inflammatory diseases (IMID) treated with biologic (bDMARDs) or synthetic targeted disease-modifying antirheumatic drugs (tsDMARDs)., Methods: An observational, descriptive, prospective and cross-sectional study of analytical prevalence analysis was conducted in patients with IMID with bDMARDs or tsDMARDs. Seroprevalence was compared by measuring immunoglobulinG (IgG) against SARS-CoV-2 between October/2020 and May/2021., Results: A total of 550 IMID's patients were studied, all of them on treatment with bDMARDs or tsDMARDs. The seroprevalence of the total patient group was 16% (88/550). Patients receiving therapy with tumor necrosis factor alpha inhibitors (TNFi) had a higher seroprevalence compared to other biologic and synthetic targeted therapies (OR: 1.792 [95%CI: 1.088-2.951]; P=.021). The influence on seroprevalence of concomitant use with b/tsDMARDs of conventional synthetic DMARDs (csDMARDs) was also analyzed. A lower seroprevalence was demonstrated in the group of patients treated with TNFi and methotrexate together, compared with those on TNFi monotherapy, 10.1 vs 24.1% (OR: 0.355 [95%CI: 0.165-0.764]; P=.006). No significant differences were found with the other DMARDs. Regarding IMIDs, no differences in seroprevalence were identified between the different disease groups., Conclusion: Patients on treatment with TNFα inhibitors have better humoral response compared to the other b/tsDMARDs. However, when associated with methotrexate the seroprevalence decreases significantly., (Copyright © 2024 Elsevier España, S.L.U. All rights reserved.)

Background: the Coronavirus disease 2019 (COVID-19) pandemic may have aggravated existing social and healthcare inequalities among particular population groups, such as ethnic minorities, who showed increased susceptibility to SARS-CoV-2 infection., Objectives: to characterize risk profiles or determinants of delayed healthcare access, as well as knowledge, risk perception, behaviour, and social stigma concerning SARS-CoV-2 infection in the immigrant population in the city of Catania (Sicily Region, Southern Italy)., Design: pilot, descriptive study., Setting and Participants: the immigrant population in Catania., Main Outcomes Measures: an ad-hoc questionnaire was prepared and administered to the participants of the target population. In addition, a web-based data collection platform and a web-based survey addressed to healthcare providers were developed., Results: 74 immigrant subjects (mean age: 39 years) voluntarily compiled the questionnaire with varying response rates per question: 77% of the participants were male, 59.5% were from Africa, 29.7% from Asia, 6.7% from South America, and 4.1% did not specify their origin. Fifty-three percent (35/66 responses) found it easy to access healthcare services. However, 25.8% (17/66 responses) found it difficult to understand written information concerning their health. Regarding vaccination services, 67.3% of subjects (35/62 responses) had no difficulty in receiving information on mandatory vaccinations and/or vaccination centres in Italy, and 79.7% (51/64 responses) were vaccinated against COVID-19. In relation to other primary prevention issues, 71.4% of participants (45/63 responses) stated they did not know or had never been tested for HIV, 64.4% (38/59 responses) declared they had not heard of or knew nothing about antibiotic resistance, and 30.4% (21/69 responses) had not heard or knew nothing about antibiotic use., Conclusions: health services seem to be accessible and effective among the immigrant population in Catania. However, identified determinants of delayed healthcare access included factors concerning mainly health literacy and possibly the socioeconomic status of the population studied. Primary prevention issues that need to be addressed due to low awareness or stigmatization among the immigrant population include antibiotic use and resistance, and infectious diseases such as HIV/AIDS.

Background: according to the literature, socially disadvantaged strata of the population, including immigrants, have been more vulnerable to the risk of SARS-CoV-2 infection due to greater exposure and less opportunity to protect themselves, and to COVID-19 complications due to metabolic and clinical risk factors as well as to healthcare access barriers. Two Italian projects - coordinated by the Italian National Institute for Health, Migration and Poverty and the Italian National Centre for Disease Prevention and Control - set up an epidemiological surveillance to monitor the temporal trends of the SARS-CoV-2 pandemic in five Italian regions using validated indicators., Objectives: to identify differences between Italians and immigrants in terms of the epidemic evolution and its health consequences, and to investigate possible differences by urbanisation degree and region of residence., Design: cross sectional study., Setting and Participants: resident population in five Italian regions: Piedmont, Emilia-Romagna, Tuscany, Lazio, and Sicily., Main Outcomes Measures: frequencies of positive tests, routine hospitalisations, and deaths related to COVID-19 were collected, with respect to the period between 22.02.2020 and 31.01.2021. Data were aggregated by week, region, degree of urbanisation, gender, age (5-year classes), and citizenship (Italian/foreigner). Crude and standardised rates of the outcomes considered were calculated, stratified by gender, citizenship, region, and aggregated by pandemic macro-period., Results: the study population counts approximately about 23 million residents as of 01.01.2020 (9.4% immigrants). During the period of interest, 1,542,458 cases of infection were recorded, whereas hospitalisations amounted to 175,979, and deaths to 44,867. Lower crude rates of hospitalisations and deaths were observed among immigrants compared to Italians. The age-standardised hospitalisation rates, on the other hand, showed an opposite trend and were significantly higher among immigrants, due to the excess observed in urban areas, especially in periods of epidemic peak, both for males (weekly mean standardised rate: 34.6 per 1,000 of foreign residents vs 24.3 of Italians over the period October 2020-January 2021) and females (23.2 vs 15.1 over the period February-April 2021). These differences seem to be more pronounced in the central regions and tend to disappear for residents in scarcely populated areas. Standardised mortality rates were higher among immigrants, both men and women, from October 2020 and more markedly in February-April 2021 among men., Conclusions: the impact of COVID-19 was stronger among immigrants in relation to hospitalisation, especially during epidemic peak periods and in some regions. The difference in the impact on mortality was smaller. There is some heterogeneity among regions and urban areas that is worth considering in the planning of interventions and integration policies.

Introduction: : Immune responses against Coronavirus (SARS-CoV-2) may be highly complex. It has been suggested that T-cell fatigue develops due to continuous stimulation of T-cells by SARS-CoV-2 in Coronavirus disease-2019 (COVID-19). It was aimed to assess peripheral lymphocyte subsets and T-cell exhaustion in various clinical courses of the disease in patients diagnosed with COVID-19., Materials and Methods: This study included 150 patients who were assigned into the "mild-to-moderate disease" group, or "severe disease" group based on their clinical and laboratory characteristics. Peripheral lymphocyte subsets and T-cell exhaustion markers [programmed cell death protein 1 (PD-1) and T-cell immunoglobulin and mucin-domain containing-3 (Tim-3)] were determined in the peripheral blood using flow cytometry., Result: Mean (±SD) age was 53.3 ± 14.5 years, and female to male ratio was 55/95. In the mild-to-moderate disease (MMD) group, 55 patients had pneumonia and 20 patients had COVID-19 without pneumonia. In the severe disease (SD) group, 43 patients had severe pneumoniae and 32 patients were in critical condition. Lymphocyte counts were less than 1.0 x 109/L in 69.3% of the patients in the SD group, and the difference between the MMD group and SD group was statistically significant (p= 0.001). Total T cells, CD4+ and CD8+ T-cell counts were significantly lower in the SD group vs. MMD group (p< 0.001, p< 0.001, p< 0.001, respectively). PD-1 expression by CD8+ and CD4 T+ cells was higher (p= 0.042, p= 0.029, respectively) and Tim-3 expression from CD4 T+ cells was lower (p= 0.000) in the SD group vs. MMD group. Serum IFN-γ levels were not statistically different in the MMD and SD groups (p= 0.2)., Conclusions: T-cell counts may be significantly reduced along with an increased expression of the T-cell exhaustion marker PD-1 in severe COVID-19, but Tim-3 expression was not increased in our study patients.

Introduction: Inmunocompromised people have higher SARS-CoV-2 morbi-mortality and they are subsidiary to receive pre-exposure prophylaxis. The objective of this study is to evaluate the effectiveness of tixagevimab/cilgavimab (Evusheld) in preventing SARS-CoV-2 infections, hospitalizations and mortality in immunocompromised patients., Materials and Methods: 119 immunocompromised people>18 years old eligible of receiving Evusheld were followed for 6 months. People with previous SARS-CoV-2 infection or incomplete vaccination regimen were exluded. A total of 19 people who received Evusheld were matched by propensity score, using a 1:1 ratio, with another 19 people who did not receive Evusheld. Sociodemographic, related to SARS-CoV-2 risk factors and related to immunosuppression variables were included. The dependent variables were infection, hospitalization, and mortality related to SARS-CoV-2. Statistical analyzes were performed using SPSS Statistics 19.0, STATA 11.0, and the R statistical package., Results: In total, 4 people in the Evusheld group and 11 in the control group had SARS-CoV-2 infection, showing an incidence rate of 3.87 and 13.62 per 100 person-months, respectively. The HR (Hazard Ratio) was 0.29 (95% CI=0.09-0.90) for SARS-CoV-2 infection, 0.37 (0.07-1.92) for SARS-CoV-2 hospitalization and, 0.23 (0.03-2.09) for SARS-CoV-2 mortality in the Evusheld group compared to control group., Conclusions: This study demonstrates that Evusheld reduces the SARS-CoV-2 infections., (Copyright © 2024 Elsevier España, S.L.U. All rights reserved.)

Introduction. During the development of the SARS-CoV-2 pandemic in Antioquia, we experienced epidemiological peaks related to the α, ɣ, β, ƛ, and δ variants. δ had the highest incidence and prevalence. This lineage is of concern due to its clinical manifestations and epidemiological characteristics. A total of 253 δ sublineages have been reported in the PANGOLIN database. The sublineage identification through genomic analysis has made it possible to trace their evolution and propagation. Objective. To characterize the genetic diversity of the different SARS-CoV-2 δ sublineages in Antioquia and to describe its prevalence. Materials and methods. We collected sociodemographic information from 2,675 samples, and obtained 1,115 genomes from the GISAID database between July 12th, 2021, and January 18th, 2022. From the analyzed genomes, 515 were selected because of their high coverage values (>90%) to perform phylogenetic analysis and to infer allele frequencies of mutations of interest. Results. We characterized 24 sublineages. The most prevalent was AY.25. Mutations of interest as L452R, P681R, and P681H were identified in this sublineage, comprising a frequency close to 0.99. Conclusions. This study identified that the AY.25 sublineage has a transmission advantage compared to the other δ sublineages. This attribute may be related to the presence of the L452R and P681R mutations associated in other studies with higher evasion of the immune system and less efficacy of drugs against SARS-CoV-2.

Significant variations have been observed in viral copies generated during SARS-CoV-2 infections. However, the factors that impact viral copies and infection dynamics are not fully understood, and may be inherently dependent upon different viral and host factors. Here, we conducted virus whole genome sequencing and measured viral copies using RT-qPCR from 9,902 SARS-CoV-2 infections over a 2-year period to examine the impact of virus genetic variation on changes in viral copies adjusted for host age and vaccination status. Using a genome-wide association study (GWAS) approach, we identified multiple single-nucleotide polymorphisms (SNPs) corresponding to amino acid changes in the SARS-CoV-2 genome associated with variations in viral copies. We further applied a marginal epistasis test to detect interactions among SNPs and identified multiple pairs of substitutions located in the spike gene that have non-linear effects on viral copies. We also analyzed the temporal patterns and found that SNPs associated with increased viral copies were predominantly observed in Delta and Omicron BA.2/BA.4/BA.5/XBB infections, whereas those associated with decreased viral copies were only observed in infections with Omicron BA.1 variants. Our work showcases how GWAS can be a useful tool for probing phenotypes related to SNPs in viral genomes that are worth further exploration. We argue that this approach can be used more broadly across pathogens to characterize emerging variants and monitor therapeutic interventions., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: NDG is a paid consultant for BioNTech, DMW has received consulting fees from Pfizer, Merck, and GSK, unrelated to this manuscript, and has been PI on research grants from Pfizer and Merck to Yale, unrelated to this manuscript., (Copyright: © 2024 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Despite impaired humoral response in patients treated with immunosuppressants (ISPs), recent studies found similar severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infection compared to controls. One potential explanation is the rapid generation of humoral response on infection, but evidence is lacking., Objectives: We investigated the longitudinal dynamics of the SARS-CoV-2 antibody repertoire after SARS-CoV-2 delta and omicron breakthrough infection in patients with immune-mediated inflammatory diseases (IMIDs) receiving ISP therapy and controls., Methods: As a prospective substudy of the national Target-to-B! (T2B!) consortium, we included IMID patients receiving ISPs therapy and controls who reported SARS-CoV-2 breakthrough infection between July 1, 2021, and April 1, 2022. To get an impression of the dynamics of the antibody repertoire, 3 antibody titers of wild-type RBD, wild-type S, and omicron RBD were measured at 4 time points after SARS-CoV-2 breakthrough infection., Results: We included 302 IMID patients receiving ISPs and 178 controls. Antibody titers increased up to 28 days after breakthrough infection in both groups. However, in IMID patients receiving therapy with anti-CD20 and sphingosine-1 phosphate receptor modulators, antibody titers were considerably lower compared to controls. In the anti-TNF group, we observed slightly lower antibody titers in the early stages and a faster decline of antibodies after infection compared to controls. Breakthrough infections were mostly mild, and hospitalization was required in less than 1% of cases., Conclusions: Most ISPs do not influence the dynamics of the SARS-CoV-2 antibody repertoire and exhibit a rapid recall response with cross-reactive antibody clones toward new virus variants. However, in patients treated with anti-CD20 therapy or sphingosine-1 phosphate receptor modulators, the dynamics were greatly impaired, and to a lesser extent in those who received anti-TNF. Nevertheless, only a few severe breakthrough cases were reported., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The COVID-19 pandemic continues to cause infections and deaths, which are attributable to the SARS-CoV-2 Omicron variant of concern (VOC). Moderna's response to the declining protective efficacies of current SARS-CoV-2 vaccines against Omicron was to develop a bivalent booster vaccine based on the Spike (S) protein from the Wuhan and Omicron BA.4/BA.5 strains. This approach, while commendable, is unfeasible in light of rapidly emerging mutated viral strains. PubMed and Google Scholar were systematically reviewed for peer-reviewed papers up to January 2024. Articles included focused on specific themes such as the clinical history of recombinant protein vaccine development against different diseases, including COVID-19, the production of recombinant protein vaccines using different host expression systems, aspects to consider in recombinant protein vaccine development, and overcoming problems associated with large-scale recombinant protein vaccine production. In silico approaches to identify conserved and immunogenic epitopes could provide broad protection against SARS-CoV-2 VOCs but require validation in animal models. The recombinant protein vaccine development platform has shown a successful history in clinical development. Recombinant protein vaccines incorporating conserved epitopes may utilize a number of expression systems, such as yeast (Saccharomyces cerevisiae), baculovirus-insect cells (Sf9 cells), and Escherichia coli (E. coli). Current multi-epitope subunit vaccines against SARS-CoV-2 utilizing synthetic peptides are unfeasible for large-scale immunizations. Recombinant protein vaccines based on conserved and immunogenic proteins produced using E. coli offer high production yields, convenient purification, and cost-effective production of large-scale vaccine quantities capable of protecting against the SARS-CoV-2 D614G strain and its VOCs., (© 2024. The Author(s), under exclusive licence to American Association of Pharmaceutical Scientists.)

Inherited deficiency of the RNA lariat-debranching enzyme 1 (DBR1) is a rare etiology of brainstem viral encephalitis. The cellular basis of disease and the range of viral predisposition are unclear. We report inherited DBR1 deficiency in a 14-year-old boy who suffered from isolated SARS-CoV-2 brainstem encephalitis. The patient is homozygous for a previously reported hypomorphic and pathogenic DBR1 variant (I120T). Consistently, DBR1 I120T/I120T fibroblasts from affected individuals from this and another unrelated kindred have similarly low levels of DBR1 protein and high levels of RNA lariats. DBR1 I120T/I120T human pluripotent stem cell (hPSC)-derived hindbrain neurons are highly susceptible to SARS-CoV-2 infection. Exogenous WT DBR1 expression in DBR1 I120T/I120T fibroblasts and hindbrain neurons rescued the RNA lariat accumulation phenotype. Moreover, expression of exogenous RNA lariats, mimicking DBR1 deficiency, increased the susceptibility of WT hindbrain neurons to SARS-CoV-2 infection. Inborn errors of DBR1 impair hindbrain neuron-intrinsic antiviral immunity, predisposing to viral infections of the brainstem, including that by SARS-CoV-2.

To understand the roles of acute-phase viral dynamics and host immune responses in post-acute sequelae of SARS-CoV-2 infection (PASC), we enrolled 136 participants within 5 days of their first positive SARS-CoV-2 real-time PCR test. Participants self-collected up to 21 nasal specimens within the first 28 days post-symptom onset; interviewer-administered questionnaires and blood samples were collected at enrollment, days 9, 14, 21, 28, and month 4 and 8 post-symptom onset. Defining PASC as the presence of any COVID-associated symptom at their 4-month visit, we compared viral markers (quantity and duration of nasal viral RNA load, infectious viral load, and plasma N-antigen level) and host immune markers (IL-6, IL-10, TNF-α, IFN-α, IFN-γ, MCP, IP-10, and Spike IgG) over the acute period. Compared to those who fully recovered, those reporting PASC demonstrated significantly higher maximum levels of SARS-CoV-2 RNA and N-antigen, burden of RNA and infectious viral shedding, and lower Spike-specific IgG levels within 9 days post-illness onset. No significant differences were identified among a panel of host immune markers. Our results suggest early viral dynamics and the associated host immune responses play a role in the pathogenesis of PASC, highlighting the importance of understanding early biological markers in the natural history of PASC.

In the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, epithelial populations in the distal lung expressing Angiotensin-converting enzyme 2 (ACE2) are infrequent, and therefore, the model of viral expansion and immune cell engagement remains incompletely understood. Using human lungs to investigate early host-viral pathogenesis, we found that SARS-CoV-2 had a rapid and specific tropism for myeloid populations. Human alveolar macrophages (AMs) reliably expressed ACE2 allowing both spike-ACE2-dependent viral entry and infection. In contrast to Influenza A virus, SARS-CoV-2 infection of AMs was productive, amplifying viral titers. While AMs generated new viruses, the interferon responses to SARS-CoV-2 were muted, hiding the viral dissemination from specific antiviral immune responses. The reliable and veiled viral depot in myeloid cells in the very early phases of SARS-CoV-2 infection of human lungs enables viral expansion in the distal lung and potentially licenses subsequent immune pathologies.

Nucleocapsid antibody assays can be used to estimate SARS-CoV-2 infection prevalence in regions implementing spike-based COVID-19 vaccines. However, poor sensitivity of nucleocapsid antibody assays in detecting infection after vaccination has been reported. We derived a lower cutoff for identifying previous infections in a large blood donor cohort (N = 142,599) by using the Ortho VITROS Anti-SARS-CoV-2 Total-N Antibody assay, improving sensitivity while maintaining specificity >98%. We validated sensitivity in samples donated after self-reported swab-confirmed infections diagnoses. Sensitivity for first infections in unvaccinated donors was 98.1% (95% CI 98.0-98.2) and for infection after vaccination was 95.6% (95% CI 95.6-95.7) based on the standard cutoff. Regression analysis showed sensitivity was reduced in the Delta compared with Omicron period, in older donors, in asymptomatic infections,

Science is humanity's best insurance against threats from nature, but it is a fragile enterprise that must be nourished and protected. The preponderance of scientific evidence indicates a natural origin for SARS-CoV-2. Yet, the theory that SARS-CoV-2 was engineered in and escaped from a lab dominates media attention, even in the absence of strong evidence. We discuss how the resulting anti-science movement puts the research community, scientific research, and pandemic preparedness at risk.

Introduction: For four years, SARS-CoV-2, the etiological agent of COVID-19, has been circulating among humans. By the end of the second year, an absence of immunologically naive individuals was observed, attributable to extensive immunization efforts and natural viral exposure. This study focuses on delineating the molecular and biological patterns that facilitate the persistence of SARS-CoV-2, thereby informing predictions on the epidemiological trajectory of COVID-19 toward refining pandemic countermeasures. The aim of this study was to describe the molecular biological patterns identified that contribute to the persistence of the virus in the human population., Materials and Methods: For over three years since the beginning of the COVID-19 pandemic, molecular genetic monitoring of SARS-CoV-2 has been conducted, which included the collection of nasopharyngeal swabs from infected individuals, assessment of viral load, and subsequent whole-genome sequencing., Results: We discerned dominant genetic lineages correlated with rising disease incidence. We scrutinized amino acid substitutions across SARS-CoV-2 proteins and quantified viral loads in swab samples from patients with emerging COVID-19 variants. Our findings suggest a model of viral persistence characterized by 1) periodic serotype shifts causing substantial diminutions in serum virus-neutralizing activity (> 10-fold), 2) serotype-specific accrual of point mutations in the receptor-binding domain (RBD) to modestly circumvent neutralizing antibodies and enhance receptor affinity, and 3) a gradually increasing amount of virus being shed in mucosal surfaces within a single serotype., Conclusion: This model aptly accounts for the dynamics of COVID-19 incidence in Moscow. For a comprehensive understanding of these dynamics, acquiring population-level data on immune tension and antibody neutralization relative to genetic lineage compositions is essential.

The ubiquitin-proteasome system is frequently employed to degrade viral proteins, thereby inhibiting viral replication and pathogenicity. Through an analysis of the degradation kinetics of all the SARS-CoV-2 proteins, our study revealed rapid degradation of several proteins, particularly NSP5. Additionally, we identified FBXO22, an E3 ubiquitin ligase, as the primary regulator of NSP5 ubiquitination. Moreover, we validated the interaction between FBXO22 and NSP5, demonstrating that FBXO22-mediated ubiquitination of NSP5 facilitated its recognition by the proteasome, leading to subsequent degradation. Specifically, FBXO22 catalyzed the formation of K48-linked polyubiquitin chains on NSP5 at lysine residues 5 and 90. Knockdown of FBXO22 resulted in decreased NSP5 ubiquitination levels, increased stability, and enhanced ability to evade the host innate immune response. Notably, the protein level of FBXO22 were negatively correlated with SARS-CoV-2 load, highlighting its importance in inhibiting viral replication. This study elucidates the molecular mechanism by which FBXO22 mediates the degradation of NSP5 and underscores its critical role in limiting viral replication. The identification of FBXO22 as a regulator of NSP5 stability provides new insights and potential avenues for targeting NSP5 in antiviral strategies., (© 2024 Wiley Periodicals LLC.)

The N121 site on the spike protein of SARS-CoV-2 is associated with heme and its metabolite, biliverdin, which can affect antibody binding. Both N121T and N121S substitutions have been observed in natural conditions and in a hamster model of dual infection with SARS-CoV-2 and Influenza A virus. Serum pseudotype neutralization assays against HIV-1 particles carrying wild-type, N121T, and N121S spikes with immune mouse and human sera revealed that N121T and N121S mutations had a greater impact on serum neutralization than biliverdin treatment. Although N121T and N121S substitutions are not currently major SARS-CoV-2 variants of concern, this study could provide fundamental information to prepare for potential future mutations at the N121 site of SARS-CoV-2., (© 2024 Wiley Periodicals LLC.)

There is growing evidence that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contaminates the marine environment and is bioaccumulated in filter-feeding shellfish. Previous study shows the Pacific oyster tissues can bioaccumulate the SARS-CoV-2, and the oyster heat shock protein 70 (oHSP70) may play as the primary attachment receptor to bind SARS-CoV-2's recombinant spike protein S1 subunit (rS1). However, detailed information about the interaction between rS1 and oHSP70 is still unknown. In this study, we confirmed that the affinity of recombinant oHSP70 (roHSP70) for rS1 (K D  = 20.4 nM) is comparable to the receptor-binding affinity of rACE2 for rS1 (K D  = 16.7 nM) by surface plasmon resonance (SPR)-based Biacore and further validated by enzyme-linked immunosorbent assay (ELISA). Three truncated proteins (roHSP70-N/C/M) and five mutated proteins (p.I229del, p.D457del, p.V491&#95;K495del, p.K556I, and p.ΣroHSP70) were constructed according to the molecular docking results. All three truncated proteins have significantly lower affinity for rS1 than the full-length roHSP70, indicating that all three segments of roHSP70 are involved in binding to rS1. Further, the results of SPR and ELISA showed that all five mutant proteins had significantly lower affinity for rS1 than roHSP70, suggesting that amino acids at these sites are involved in binding to rS1. This study provides a preliminary theoretical basis for the bioaccumulation of SARS-CoV-2 in oyster tissues or using roHSP70 as the capture unit to selectively enrich virus particles for detection., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The N-terminal domain (NTD) of the SARS-CoV-2 S protein comprises five exposed protruding loops. Deletions, insertions, and substitutions within these NTD loops play a significant role in viral evolution and contribute to immune evasion. We reported previously that introducing the glycan masking mutation R158N/Y160T in the NTD loop led to increased titers of neutralizing antibodies against the SARS-CoV-2 Wuhan-Hu-01 strain, as well as the Alpha, Beta, and Delta variants. In this study, we conducted further investigations on 10 additional glycan-masking sites in the NTD loops. Our findings indicate that the introduction of glycan masking mutations, specifically N87/G89T, H146N/N148T, N185/K187T, and V213N/D215T significantly enhanced neutralizing antibody titers against the Delta variant. The combination of dual glycan-masking mutations R158N/Y160T+V213N/D215T and R158N/Y160T+G219N results in a shift toward the Omicron BA.1. Furthermore, the introduction of the Omicron receptor binding domain (RBD) alongside these two dual glycan masking mutations of Wuhan-Hu-1 and XBB.1 NTD sequences resulted in a noticeable shift in antigenic distances, aligning with the Omicron BA.4/5, BA.2.75.2, BQ.1.1, and XBB.1 subvariants on the antigenic map. This strategic combination, which involves the dual glycan masking mutations R158N/Y160T+V213N/D215T and R158N/Y160T+G219N in the NTD loops, along with the domain swap incorporating the Omicron RBD, emerges as a promising vaccine design strategy for the continuous development of next-generation SARS-CoV-2 vaccines., (© 2024 Wiley Periodicals LLC.)

Commercially available assays for measuring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) anti-spike (S) or anti-nucleocapsid (N) antibodies differ in units, making results comparisons challenging. This study aimed to develop conversion equations between five quantitative anti-S antibody tests and to assess the agreement over time between three qualitative anti-N antibody tests. Blood samples from 24 216 vaccinated healthcare workers in Hiroshima Prefecture, Japan, were analyzed for anti-S antibodies using five quantitative tests (Abbott, Fujirebio, Ortho, Sysmex, Roche) and for anti-N antibodies using three qualitative tests (Abbott, Sysmex, Roche). Geometric mean regression was performed to establish equations for converting measured values between the five quantitative tests. Fleiss κ statistic was used to assess the agreement between the three qualitative tests. A strong correlation (Pearson's coefficient r > 0.9) was found for each pair of the five quantitative tests measuring anti-S antibodies, enabling the development of equations to convert values between each pair. Using these equations, which are based on the original output unit of each test, values obtained from one test can be transformed to be equivalent to the corresponding values in another test. For the three tests for anti-N antibodies, the agreement was substantial in the total sample (Fleiss' κ, 0.74) and moderate among those with self-reported past coronavirus disease 2019 (COVID-19) infection (Fleiss' κ, 0.39). The agreement decreased with time after infection. Reduced agreement between anti-N antibodies tests over time suggests caution in comparing seroepidemiological studies of COVID-19 exposure based on anti-N antibodies measurement. The findings could help improve antibody measurement systems and inform public health decision-makers., (© 2024 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.)

Background: The objective of the present study is to analyze the epidemiological, clinical and functional characteristics of patients admitted to the University Hospital of Navarra due to SARS-CoV-2 infection, as well as the predictors of mortality, during the first wave of the pandemic caused by this virus., Methodology: An observational, retrospective study was performed, including all hospitalized patients older than 75 years. Information has been obtained on multiple variables, among which it is worth mentioning previous geriatric syndromes or those that have appeared during hospitalization, or past medical history considered relevant in SARS-CoV-2 infection. A descriptive analysis of the data, comparisons according to various factors of interest and multivariate analysis to analyze factors associated with mortality were carried out., Results: Data have been obtained from a total of 426 patients with a mean age of 83.2 years (52.6% men). 34.7% died in hospital and 4.5% within 1 month after hospital discharge. The factors related to mortality were: worse baseline functional status, chronic kidney disease, and fever or dyspnea as forms of presentation. The most frequent typical symptoms were: fever, dyspnea, cough, asthenia and hyporexia. Up to 42.1% presented delirium as a symptom of atypical onset. We observed a functional deterioration that was not recover after a month of follow-up (baseline Barthel index 81.12; 70.08 at discharge; 75.55 after a month)., Conclusions: SARS-CoV-2 infection has caused high mortality rates in older adults. In this age group, the atypical presentation of this disease and functional deterioration during hospitalization are frequent. In the present study, a worse previous functional status has been identified as a predictor of mortality. More studies are needed to evaluate the impact that the disease and hospitalization have on the older patient, with the aim of implementing preventive, diagnostic and therapeutic measures that are necessary to avoid functional deterioration and adverse health events related to it., (Copyright © 2023 SEGG. Publicado por Elsevier España, S.L.U. All rights reserved.)

Introduction: It is often discussed that a positive PCR for SARS-CoV-2 in hospitalized patients may not be causally linked to the hospital stay, but no scientific data are available from Germany. Therefore, we analyzed to what extent a positive PCR test could be assessed as causal or secondary to admission according to clinical criteria in a tertiary care hospital of the first 4 months of 2022., Methods: SARS-CoV-2-positive patients of RoMed-Klinikum Rosenheim/Bavaria from 01/01/2022 to 30/04/2022 were included. Patients were divided into a group with COVID-19 as direct reason for admission (CAW), and a group, in which this did not apply according to a comprehensive clinical assessment (nCAW). Patients with no clear allocation to these groups were counted separately. Categorization was based on a multilevel procedure and performed by an internist experienced in COVD-19 (M.H.). It included all available clinical, radiological, and laboratory findings as well as treatment decisions., Results: 647 cases were included (age 10 days to 101 years, median 68 years; 49.5% women), including 13 patients in two admissions with positive PCR. 45.3% (n=293) were attributable to the group with COVID as the reason for admission, 48.8% (n=316) were not, no clear decision could be made in 35 patients, 3 patients were transferred from other clinics for isolation. In infants (up to 1 year), a positive PCR test was more frequently categorized as causative than in older patients. Leading symptoms of classification were found to be fatigue/fatigue, fever/chills, and cough on admission. Febrile convulsions accounted for the reason for admission in 10 cases of children (age 1.1-7.6 years). Length of stay did not differ significantly between groups (median (quartiles) 5 (2; 10) days for CAW, 5 (2; 12) for nCAW), nor did in-hospital mortality and median age of deceased or survivors., Discussion: A retrospective analysis of all clinical data revealed that positive SARS-CoV-2 PCR played a major and - according to clinical criteria - causative role for admission and hospitalization in nearly 50% of cases, whereas it was an incidental finding in just under 50%. These results confirm data from other countries and demonstrate that the role of a positive SARS-CoV-2 PCR test for hospitalization can only be answered by a comprehensive and elaborate analysis of individual data., Competing Interests: Die Autorinnen/Autoren geben an, dass kein Interessenkonflikt besteht., (Thieme. All rights reserved.)