Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

Comprehensive analysis of human coronavirus antibody responses in ICU and non-ICU COVID-19 patients reveals IgG3 against SARS-CoV-2 spike protein as a key biomarker of disease severity

Introduction. Pre-existing immunity to human coronaviruses (HCoVs) may shape the immune response in COVID-19 patients. Increasing evidence suggests that immune cross-reactivity between SARS-CoV-2 and other coronaviruses may determine clinical prognosis.Hypothesis. SARS-CoV-2 disease severity is influenced by pre-existing immunity to HCoVs, with distinct antibody profiles and cross-reactivity patterns.Aim. To investigate the antibody response of ICU and non-ICU SARS-CoV-2 patients against different HCoV proteins and assess the potential impact of pre-existing immunity on SARS-CoV-2 disease outcomes.Methodology. This study used a comprehensive HCoVs antigen bead array to measure antibody response to pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, SARS-CoV-2 and the four seasonal HCoVs in 70 ICU and 63 non-ICU COVID-19 patients.Results. Our analysis demonstrates an overall higher antibody response in ICU than in non-ICU COVID-19 patients. Interestingly, the anti-S1 IgG and IgA were significantly higher among ICU than in non-ICU patients. Similarly, the anti-S1 IgG against NL63 showed a lower response among ICU compared to non-ICU. Cross-reactivity was evident between SARS-CoV-2 and SARS-CoV antibodies but not with MERS-CoV and seasonal HCoVs. The subclass analysis of antibodies recognizing SARS-CoV-2 revealed that anti-S1 IgG1, IgG3, IgA1 and IgA2 were significantly higher in ICU compared to non-ICU. The predominant IgA subtype among SARS-CoV-2 patients was IgA1. We applied machine learning algorithms to subclass serological responses to build classifiers that could distinguish between ICU patients and patients with milder COVID-19. Out of 90 variables used in two different types of models, the variable of highest influence in determining the ICU status was IgG3 against SARS-CoV-2 S, and the top 8 variables of influence included the presence of IgG3 against S-trimer as well as IgA against SARS-CoV-2 S.Conclusion. Understanding the complexities of humoral immunity in various patients is critical for early medical intervention, disease management, selective vaccination and passive immunotherapy.

Corticosteroids and long-term pulmonary function after critical illness due to COVID-19- a single-center cohort study

BACKGROUND

Early in the pandemic, corticosteroids became standard treatment for patients with critical COVID-19 infections. This study aimed to investigate the possible long-term pulmonary consequences after corticosteroid treatment in patients with critical COVID-19 requiring ventilatory support.

METHODS

This observational single-center cohort study included patients treated for critical COVID-19 requiring ventilatory support between March 1, 2020, and August 1, 2021, with a 6-month follow-up after discharge from the intensive care unit. Corticosteroid treatment was defined according to the RECOVERY trial (6 mg dexamethasone daily or equivalent dose of another corticosteroid, initiated within eight days of hospital admittance and continued for at least one day) Pulmonary function was assessed by diffusion capacity for carbon monoxide. Health-related quality of life was measured with the questionnaire RAND-36. General linear regression was used to present mean score differences with 95% confidence intervals.

RESULTS

Among the 456 (69%) critically ill COVID-19 patients who survived at least 90 days after ICU discharge, 286 (63%) attended the follow-up six months later. The groups were balanced regarding invasive ventilation; 47% received invasive ventilation in both groups. Corticosteroid treatment was associated with a lower diffusion capacity for carbon monoxide (MSD - 8.3, 95% CI: -14.2 to -2.4) 6 months after ICU discharge (change > 10% were regarded as clinically significant). There were no differences in health-related quality of life between the groups.

CONCLUSIONS

Corticosteroids might negatively impact pulmonary function after critical COVID-19. The decrease did not seem to influence health-related quality of life. Future studies are needed to confirm the results.

Multisystem inflammatory syndrome in children and Kawasaki disease

This narrative review aims to analyze and compare the current literature on multisystem inflammatory syndrome in children (MIS-C) and Kawasaki disease (KD), with a focus on case definitions, clinical features, diagnostic approaches, treatment strategies, and outcomes. Through a comprehensive review of relevant studies, including screening titles, abstracts, and full-text articles, key similarities and differences were identified. Both MIS-C and KD involve immune system dysregulation and share clinical manifestations such as rash, gastrointestinal symptoms, and cardiovascular involvement, with treatments often centered around immunomodulatory therapies. However, significant differences were observed, particularly in terms of age distribution, demographic prevalence, clinical presentation, and diagnostic criteria, with KD primarily affecting younger children and being associated more prominently with coronary artery abnormalities. While both diseases raise concerns about severe cardiac involvement and the need for intensive care, their pathogenic mechanisms have not been fully understood. Ongoing research is critical to elucidating these mechanisms, refining diagnostic criteria, and optimizing therapeutic approaches to improve outcomes for affected children. This comparative analysis is essential for advancing the understanding of both conditions, as accurately distinguishing between MIS-C and KD has significant implications for clinical decision-making and patient management. Given their overlapping yet distinct clinical features, precise differentiation is critical for ensuring timely diagnosis, optimizing therapeutic strategies, and improving patient outcomes. The concern among pediatric patients stems from the potential for severe complications, particularly cardiac involvement, which underscores the need for heightened awareness, early recognition, and evidence-based treatment strategies to minimize long-term morbidity and mortality.

Insights into COVID-19 epidemiology and control from temporal changes in serial interval distributions in Hong Kong

The serial interval (SI) distribution of an epidemic is used to approximate the generation time distribution, an essential parameter for inferring the transmissibility (${R}_t$) of an infectious disease. However, SI distributions may change as an epidemic progresses. We examined detailed contact tracing data on laboratory-confirmed cases of COVID-19 in Hong Kong, China, during the 5 COVID-19 waves from January 2020 to July 2022. We reconstructed the transmission pairs and estimated time-varying effective SI distributions and factors associated with longer or shorter intervals. Finally, we assessed the biases in estimating transmissibility using constant SI distributions. We found clear temporal changes in mean SI estimates within each epidemic wave studied and across waves, with mean SIs ranging from 5.5 days (95% credible interval, 4.4-6.6) to 2.7 days (95% credible interval, 2.2-3.2). The mean SIs shortened or lengthened over time, which was found to be closely associated with the temporal variation in COVID-19 case profiles and public health and social measures and could lead to biases in predicting ${R}_t$. Accounting for the impact of these factors, the time-varying quantification of SI distributions could lead to improved estimation of ${R}_t$, and could provide additional insights into the impact of public health measures on transmission.

Rebound Hypoxemia in Mechanically Ventilated Patients With COVID-19 Completing a Standard 10-Day Course of Corticosteroid Therapy

Background: Rebound hypoxemia may occur after cessation of corticosteroid therapy for COVID-19 pneumonitis. We aimed to determine the incidence of this phenomenon in mechanically ventilated patients with COVID-19 completing corticosteroid therapy. Methods: We conducted a retrospective observational cohort study across 2 tertiary ICUs from September to December 2021. We included all adult patients receiving invasive mechanical ventilation on completion of a 10-day course of dexamethasone for COVID pneumonitis. Our primary outcome was change in PaO2/FIO2 ratio in the 7 days following cessation of dexamethasone. Secondary outcomes included duration of ventilation, frequency of corticosteroid recommencement, and mortality. Results: We studied 88 subjects. Median age was 61 years (interquartile range [IQR] 51-67), and median duration of mechanical ventilation was 14 days (IQR 11-26). On completion of dexamethasone, 62 subjects (70%) remained off corticosteroid therapy for the subsequent 7 days. Of these, 63% (n = 20) had a stable PaO2/FIO2 ratio on day 7 (mean change 197 ± 42 mm Hg to 258 ± 83 mm Hg). Subjects who had a reduction in PaO2/FIO2 ratio >20 mm Hg by day 7 (mean change 214 ± 68 mm Hg to 152 ± 78 mm Hg) were more likely to die in hospital (P < .001). These subjects had a higher C-reactive protein level at time of steroid cessation (204 ± 87 mg/L, P = .17), which remained persistently elevated (206 ± 89 mg/L, P = .01) on day 7. The 30% of subjects who recommenced steroids required a longer duration of ventilation (13.5 vs 24.5 d, P = .002) but showed no differences in ICU mortality (19% vs 27%, P = .43). Conclusions: Rebound hypoxemia and steroid recommencement were common occurrences in mechanically ventilated subjects with COVID-19. Rebound hypoxemia was associated with higher mortality. Steroid recommencement was associated with longer duration of mechanical ventilation but no significant difference in mortality.

Flow cytometric analysis of the SARS coronavirus 2 antibodies in human plasma

COVID-19 is an infectious disease caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2). Anti-SARS-CoV-2 antibodies can provide information on patient immunity, identify asymptomatic patients, and track the spread of COVID-19. Efforts have been made to develop methods to detect anti-SARS-CoV-2 antibodies in humans. Here, we describe a flow cytometric assay for the simultaneous detection of anti-SARS-CoV-2 IgG and IgM in human plasma. To assess the antibody response against the different SARS-CoV-2 structural proteins, five viral recombinant proteins, including spike protein subunit 1 (S1), N-terminal domain of S1 (S1A), spike receptor-binding domain (RBD), spike protein subunit 2 (S2), and nucleocapsid protein (N), were generated. A comparison of the antibody profiles detected by the assay with plasma from 100 healthy blood donors collected prior to the COVID-19 pandemic and plasma from 100 virologically confirmed COVID-19 patients demonstrated a clear discrimination between the two groups. Among the COVID-19 patients, the antibody responses for the viral proteins, as determined by their prevalence, were anti-RBD IgG = anti-N IgG > anti-S1 IgG > anti-S1A IgG > anti-S2 IgG, and anti-RBD IgM > anti-S1 IgM > anti-N IgM > anti-S2 IgM. The prevalence of anti-SARS-CoV-2 IgG and IgM was not associated with sex, age, race, days after the onset of symptoms, or severity of illness, except for a higher prevalence of anti-S2 IgG being observed in men than in women. The levels of anti-RBD IgG were higher in patients 65 years and older and in patients who had severe symptoms. Similarly, patients who had severe symptoms exhibited higher levels of anti-S1 and anti-S1A IgG than patients who had mild or moderate symptoms. The levels of anti-RBD IgM tended to be higher in men but did not differ among age, race, days after the onset of symptoms, or severity of illness. Our study indicates that the flow cytometric assay, especially using RBD as target antigen, can be used to detect simultaneously anti-SARS-CoV-2 IgG and IgM antibodies in human plasma.

Bacterial lysates in modifying sIgA levels in the upper respiratory tract in COVID-19 patients

A great deal of evidence has accumulated suggesting an important role of mucosal immunity not only in preventing COVID-19 but also in the pathogenesis of this infection. The aim of the study was to evaluate the levels of secretory immunoglobulin A (sIgA) in different compartments of the upper respiratory tract in COVID-19 patients in relation to the severity of the disease and treatment with a bacteria-based immunomodulating agent (Immunovac VP4). The titers of sIgA were determined by ELISA in nasal epithelial swabs, pharyngeal swabs, and salivary gland secretions at baseline and on days 14 and 30 of treatment. The levels of nasal, pharyngeal and salivary sIgA were significantly lower in more severe patients (subgroup A) than in less severe patients (subgroup B), p < 0.01. In subgroup A, the patients who received Immunovac VP4 had higher pharyngeal sIgA levels in convalescent period than those who did not receive the therapy p < 0.05. In subgroup B patients, an increase in immunoglobulin levels was observed from baseline to day 14 of treatment whether they received the add-on therapy or not, p < 0.01. On day 30 of treatment, the sIgA levels in the standard treatment group, however, decreased, while the patients receiving the immunomodulating agent maintained high sIgA levels, p < 0.05. Oxygen saturation significantly increased by day 14 in both groups, p < 0.001. However, it was higher in the Immunovac VP4 group than in the standard treatment group, p < 0.01. Thus, addition of a bacterial lysate-based immunomodulating agent to the treatment regimen for moderate-to-severe COVID-19 induces the production of pharyngeal and salivary sIgA. SIgA production is inversely correlated to CRP levels and percentage of lung involvement on CT scan and is directly correlated to SpO2 levels.

Evaluation of the effects of pre-exposure treatment with hydroxychloroquine on the risk of COVID-19 infection and on the efficacy of anti-COVID-19 vaccination during lupus or Gougerot-Sjögren's disease: Prepcov multicentre trial

OBJECTIVES

Some patients with SLE or Gougerot-Sjögren's disease (GSD) receive long-term treatment with hydroxychloroquine (HCQ), sometimes combined with immunosuppressive therapy (IS). This study sought to assess whether long-term HCQ therapy that had been initiated long before the COVID-19 pandemic had a protective or adverse effect on COVID-19 risk, severity of infection or immunity protection.

METHODS

This prospective multicentre study included 547 patients with SLE, GSD, autoimmune hepatitis, primary biliary cholangitis or cured viral hepatitis C divided into four groups according to HCQ (+/-) and IS (+/-) intake prior to the pandemic: HCQ+IS+ (n=112), HCQ+IS- (n=121), HCQ-IS+ (n=115) and HCQ-IS- (n=199). When COVID-19 vaccination was possible, patients were vaccinated as recommended. Vaccination efficacy was prospectively assessed on the basis of the postvaccination antibody titre.

RESULTS

Compared with HCQ+IS+ patients, HCQ-IS+ patients had a decreased risk of COVID-19 infection (p<0.001). Compared with HCQ+IS+ patients, HCQ-IS- patients had a decreased risk of contracting COVID-19 (p<0.001). Patients in the HCQ-IS+ or HCQ-IS- group had a lower risk of symptomatic or severe infection than HCQ+IS+ patients did (p=0.001 and p<0.001, respectively). Only patients who had two or more exposures (to vaccine and/or infection) had an increased likelihood of COVID-19 immunity after the last dose (p<0.001).

CONCLUSIONS

HCQ treatment that was initiated before the pandemic did not protect against COVID-19 infection. Moreover, non-exposure to HCQ treatment (combined or not with IS) was associated with decreased risk of COVID-19 infection and of developing a symptomatic or severe infection. HCQ and IS do not influence the vaccine response. Only two or more doses of vaccine result in a good vaccine response.

TRIAL REGISTRATION NUMBER

NCT04481633.

Modeling the spatiotemporal transmission of COVID-19 epidemic by coupling the heterogeneous impact of detection rates: A case study in Hong Kong

During the COVID-19 epidemic, many infections may have been undiagnosed in communities (hidden cases) due to low detection rates, thus exacerbating the overall prevalence of the epidemic. However, the heterogeneity of detection rates poses a challenge in simulating the proportion and spatial distribution of hidden cases. Coupling the heterogeneous impact of detection rates to extend epidemic modeling is necessary for forecasting the health burden and mitigating the inequity of testing resources. In this study, we developed an agent-based model integrated with the Susceptible-Exposed-Reported-Hidden-Removed (SERHR) model to simulate the spatiotemporal transmission of reported and hidden cases (RH-ABM). The RH-ABM was fitted with data for the fifth wave of infection in Hong Kong induced by the Omicron variant. We conducted multi-scenario simulations based on various testing strategies to assess the local variation in attack rates. The RH-ABM predicted that maintaining a constant high detection rate would reduce the average attack rate from 65.62% to 53.09%. Increasing detection rates in groups with many individuals and daily close contact can also assist in controlling the health burden of outbreaks. The variation in the attack rates is strongly associated with changes in the region-stratified detection rates. In addition, The RH-ABM estimated that allocating limited testing resources based on demographic distribution and human mobility data is effective for controlling the average attack rate.

Ultrasensitive Specific Detection of Anti-influenza A H1N1 Hemagglutinin Monoclonal Antibody Using Silicon Nanowire Field Effect Biosensors

Rapid and sensitive detection of virus-related antigens and antibodies is crucial for controlling sudden seasonal epidemics and monitoring neutralizing antibody levels after vaccination. However, conventional detection methods still face challenges related to compatibility with rapid, highly sensitive, and compact detection apparatus. In this work, we developed a Si nanowire (SiNW)-based field-effect biosensor by precisely controlling the process conditions to achieve the required electrical properties via complementary metal-oxide-semiconductor (CMOS)-compatible nanofabrication processes. The SiNW surface was chemically modified with 2-aminoethylphosphonic acid, followed by a dehydration condensation reaction with influenza A H1N1 hemagglutinin (HA1), to enable specific detection of anti-HA1 immunoglobulin G (IgG). We successfully detected the anti-influenza IgG with concentrations ranging from 1 aM to 100 nM, achieving a remarkable detection limit of 6.0 aM. To demonstrate specificity, a control experiment was conducted using normal mouse IgG with concentrations of 6 aM to 600 nM. The results showed a high specificity, with the signal being 6-fold greater for the target IgG compared to the control IgG. This work demonstrates the capability of SiNW biosensors to detect anti-influenza A H1N1 hemagglutinin monoclonal antibody with enhanced detection sensitivity and specificity. This work lays the groundwork for future applications in detecting antibodies after vaccination or immunotherapy, contributing to the effective management of infectious pandemics.

SARS-CoV-2 Infection Among Children in Rondônia, Western Brazilian Amazon: SARS-CoV-2 Among Children in Rondônia

We analyzed 364 children symptomatic or asymptomatic for respiratory symptoms, aged 0.1 month-17 years, selected from primary healthcare units of different municipalities of Rondônia from June 2021 to September 2022. Data were collected from medical and electronic records for epidemiological characterization. The positive cohort (n = 96) was quantified using a real-time (RT) qPCR and sequenced by next-generation sequencing. Whole-genome sequences were obtained, SARS-CoV-2 strains were classified using the Pango system, and the maximum likelihood method was used for phylogenetic analyses. Among the patients, 59.34% (216/364) were male and 40.66% (148/364) were female. Children aged 10-14 years showed the highest rate of SARS-CoV-2 positivity. At the time of collection, 54.12% (197/364) of the patients were not age-eligible for immunization against COVID-19. The unvaccinated group accounted for 34.07% (124/364), with the highest proportion in the age groups of 5-9 and 10-14 years. Most patients exhibited mild symptoms. Seventy-nine high-quality genomes were obtained: Delta variant of concern (VOC) was the most prevalent (most abundant strain: AY.99.2), Omicron VOC was reported in 26 individuals (most frequent subvariant: BA.1.1), and Gamma VOC with 22 cases (12 cases of P.1 strain). The viral load showed a median of 7.26 log10 copies/mL, with a mean symptom duration of 4 days. Most of the cases were from children who were unvaccinated and age-ineligible for immunization and were associated with Delta and Omicron VOCs with an increase in subvariants during the study period.

Quantification of droplet and contact transmission risks among elementary school students based on network analyses using video-recorded data

In elementary schools, immunologically immature students come into close contact with each other and are susceptible to the spread of infectious diseases. To analyze pathogen transmission among students, it is essential to obtain behavioral data. Questionnaires and wearable sensor devices were used for communication behavior and swab sampling was employed for contact behavior. However, these methods have been insufficient in capturing information about the processes and actions of each student that contribute to pathogen transmission. Therefore, in this study, actual behavioral data were collected using video recordings to evaluate droplet and contact transmission in elementary schools. The analysis of communication behavior revealed the diverse nature of interactions among students. By calculating the droplet transmission probabilities based on conversation duration, the risk of droplet transmission was quantified. In the contact behavior, we introduced a novel approach for constructing contact networks based on contact history. According to this method, well-known items, such as students' desks, doors, and faucets, were predicted to be potential fomite. In addition, students' shirts and shared items with high contact frequency and high centrality metrics in the network, which were not evaluated in swab sampling surveys, were identified as potential fomites. The reliability of the predictions was demonstrated through micro-simulations. The micro-simulations replicated virus transmission scenarios in which virus-carrying students were present in the actual contact history. The results showed that a significant amount of virus adhered to the items predicted to be fomites. Interestingly, the micro-simulations indicated that most viral copies were transmitted through single items. The analysis of contact history, contact networks, and micro-simulations relies on video-recorded behavioral data, highlighting the importance of this method. This study contributes significantly to the prevention of infectious diseases in elementary schools by providing evidence-based information about transmission pathways and behavior-related risks.

Comparative study of alpha, beta, and omicron spike protein by computing the IR/Raman frequencies and UV-vis adsorption - A computational analysis through DFT

The outbreak of COVID-19 coronavirus disease around the end of 2019 was a pandemic. The virus has been mutated and so many strains like Alpha, Beta, and Omicron are present in different parts of the world. Hence, timely detection technique is important to overcome the diagnostic challenges. Considering the need for this pandemic situation, we used a spectroscopy test methodology to distinguish different strains of Covid-19 by computing the infrared & Raman frequencies and the optical absorption data. Optimization of spike protein of Alpha, and Omicron mutations showed the high value of dipole moment (4.44, and 4.36) Debye, and polarizability [Alpha (233.62), Omicron (228.65)] indicating more bioactivity of Alpha and Omicron instead of Beta. Molecular electrostatic potential map exhibits the presence of electrophilic and nucleophilic region suggesting charge transfer of spikes to accept/donate electrons and hence the system increased reactiveness. UV-Vis absorption analysis also shows electronic transitions (σ to π∗ and π to π∗) due to that protein probe mechanism of Alpha and Omicron becomes increasingly become unsaturated thus confirming its easy binding ability to the target human protein as compared to binding affinity of Beta spike protein.

Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load

Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time and magnitude of these host responses were significantly correlated to viral load.

SARS-CoV-2 specific adaptations in N protein inhibit NF-κB activation and alter pathogenesis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and severe acute respiratory syndrome coronavirus (SARS-CoV) exhibit differences in their inflammatory responses and pulmonary damage, yet the specific mechanisms remain unclear. Here, we discovered that the SARS-CoV-2 nucleocapsid (N) protein inhibits the activation of the nuclear factor-κB (NF-κB) pathway and downstream signal transduction by impeding the assembly of the transforming growth factor β-activated kinase1 (TAK1)-TAK1 binding protein 2/3 (TAB2/3) complex. In contrast, the SARS-CoV N protein does not impact the NF-κB pathway. By comparing the amino acid sequences of the SARS-CoV-2 and SARS-CoV N proteins, we identified Glu-290 and Gln-349 as critical residues in the C-terminal domain (CTD) of the SARS-CoV-2 N protein, essential for its antagonistic function. These findings were further validated in a SARS-CoV-2 trans-complementation system using cellular and animal models. Our results reveal the distinctions in inflammatory responses triggered by SARS-CoV-2 and SARS-CoV, highlighting the significance of specific amino acid alterations in influencing viral pathogenicity.

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Pregnant Women Treated with Nirmatrelvir/Ritonavir (Paxlovid) Using Salivary Polymerase Chain Reaction: A Prospective Cohort Study

OBJECTIVES

We aim to study the relative viral load using salivary polymerase chain reaction among pregnant women treated with Paxlovid.

METHODS

Pregnant women with coronavirus disease 2019 were allocated to two groups: those receiving Paxlovid and those receiving no antiviral agents. We compared the nasopharyngeal and salivary relative viral loads and their changes in saliva specimens.

RESULTS

Among the thirty-seven pregnant women, seventeen received Paxlovid, and twenty received no antiviral agents. The viral cycle threshold value of saliva was significantly higher than that from nasopharynx, with a median ± interquartile range of 26.44 ± 7.68 versus 17.6 ± 9.6 in the Paxlovid group (p = 0.005). Following treatment, the median salivary viral load decreased by 13.40 cycle threshold values in the Paxlovid group (from a median of [Day 0 Ct] to [Day 4/5 Ct]), compared to a change of -1.59 cycle threshold values in the no-antiviral group (from a median of [Day 0 Ct] to [Day 4/5 Ct]) (p = 0.021). The detection rate of coronavirus disease 2019 using salivary polymerase chain reaction was 83.8% (31/37).

CONCLUSIONS

This study showed that saliva is a useful diagnostic tool for coronavirus disease 2019 in pregnant women, and a significant decrease in the relative viral load of saliva was observed in those treated with Paxlovid.

Association of SARS-CoV-2 immunoserology and vaccination status with myocardial infarction severity and outcome

BACKGROUND

The COVID-19 pandemic adversely affected the severity and prognosis of patients with acute myocardial infarction (MI) caused by atherothrombosis (type 1 MI). The effect, if any, of COVID-19 vaccination and natural SARS-CoV2 serologic immunity in these patients is unclear. Our aim was to analyze the association between the severity and outcome of patients with type 1 MI and their previous SARS-CoV2 vaccination and serostatus.

METHODS

A single-center retrospective cohort study conducted between March 1, 2020 and March 1, 2023. Clinical and follow-up information was collected from medical records and patients. Total antibodies (IgM, IgA, IgG) to nucleocapsid (N) antigens were measured by ECLIA (electrochemiluminescence-based immunoassay) to test the immune response to natural infection. If positive, IgM and IgG antibodies to spike (S) surface antigens were measured by CLIA to test the immune response to vaccine or natural infection. Multivariable logistic regression analysis was performed, adjusting for age, sex, hypertension, diabetes, and dyslipidemia.

RESULTS

Total sample of 949 patients, 656 with ST-segment elevation MI (STEMI) and 293 with non-ST-segment elevation MI (NSTEMI). Mean age was 64 (SD 13) years, 80 % men. Pre-admission vaccination status was: ≥ 1 dose, 53 % of patients; complete vaccination, 49 %; first booster dose, 25 %. The majority (84 %) of vaccines administered were mRNA-based. Six months after MI, 92 (9.7 %) patients had a major adverse cardiac event (MACE) and 50 died; 11 % of patients had severe heart failure or cardiogenic shock (Killip III-IV) after STEMI. Vaccinated patients with STEMI and positive serology (Pos/Vax group) had a higher risk of Killip III-IV on admission: OR 2.63 (1.27-5.44), p = 0.010. SARS-CoV-2 S-specific IgG titers were highest in this group (median > 2080 AU/mL, [IQR 1560- >2080] vs 91 [32-198] in the unvaccinated group). In the overall sample, a higher incidence of 6-month MACE was not demonstrated (OR 1.89 [0.98-3.61], p = 0.055).

CONCLUSIONS

The combination of vaccination and natural SARS-CoV2 infection was associated with the development of severe heart failure and cardiogenic shock in patients with STEMI, possibly related to an increased serological response.

MDA5 Is a Major Determinant of Developing Symptoms in Critically Ill COVID-19 Patients

Apart from the skin and mucosal immune barrier, the first line of defense of the human immune system includes MDA5 (ifih1 gene) which acts as a cellular sensor protein for certain viruses including SARS-CoV-2. Upon binding with viral RNA, MDA5 activates cell-intrinsic innate immunity, humoral responses, and MAVS (mitochondrial antiviral signaling). MAVS signaling induces type I and III interferon (IFN) expressions that further induce ISGs (interferon stimulatory genes) expressions to initiate human cell-mediated immune responses and attenuate viral replication. SARS-CoV-2 counteracts by producing NSP1, NSP2, NSP3, NSP5, NSP7, NSP12, ORF3A, ORF9, N, and M protein and directs anti-MDA5 antibody production presumably to antagonize IFN signaling. Furthermore, COVID-19 resembles several diseases that carry anti-MDA5 antibodies and the current COVID-19 vaccines induced anti-MDA5 phenotypes in healthy individuals. GWAS (genome-wide association studies) identified several polymorphisms (SNPs) in the ifih1-ifn pathway genes including rs1990760 in ifih1 that are strongly associated with COVID-19, and the associated risk allele is correlated with reduced IFN production. The genetic association of SNPs in ifih1 and ifih1-ifn pathway genes reinforces the molecular findings of the critical roles of MDA5 in sensing SARS-CoV-2 and subsequently the IFN responses to inhibit viral replication and host immune evasion. Thus, MDA5 or its pathway genes could be targeted for therapeutic development of COVID-19.

Urban wastewater contains a functional human antibody repertoire of mucosal origin

Wastewater-based surveillance of human disease offers timely insights to public health, helping to mitigate infectious disease outbreaks and decrease downstream morbidity and mortality. These systems rely on nucleic acid amplification tests for monitoring disease trends, while antibody-based seroprevalence surveys gauge community immunity. However, serological surveys are resource-intensive and subject to potentially long lead times and sampling bias. We identified and characterized a human antibody repertoire, predominantly secretory IgA, isolated from a central wastewater treatment plant and building-scale wastewater collection points. These antibodies partition to the solids fraction and retain immunoaffinity for SARS-CoV-2 and Influenza A virus antigens. This stable pool could enable real-time tracking for correlates of vaccination, infection, and immunity, aiding in establishing population-level thresholds for immune protection and assessing the efficacy of future vaccine campaigns.

Evaluation of rapid detection methods for H5N1 virus using biosensors: An AI-based study

High mortality and zoonotic potential predispose the H5N1 avian influenza virus as a critical threat. knowing that an epidemic could be occurring, quick and precise diagnostic techniques are essential for managing and containing possible epidemics. To detect H5N1 in saliva samples, this study investigates the theoretical design, simulation and evaluation of three kind of biosensors based on different technologies with potential as rapid identifications tools to diagnose quickly H5N1: Lateral Flow Tests (LFT), Field Effect transistors (FET) based electrochemical sensors and Quartz Crystal Microbalance (QCM) sensors. Through detailed AI-based simulations, we show the capabilities, sensitivities and specificities of these biosensors, highlighting their potential for applications in general biology as well as their suitability both for routine home practice and for applications by control entities in public settings. We therefore wish to pave the way to a framework for the quick creation of detection tools that can be swiftly implemented for rapid deployment in case of an outbreak of disease.

Predicting severe COVID-19 using readily available admission indicators: SpO2/FiO2 ratio, comorbidity index, and gender

The focus of this study was to identify risk factors for severe and critical COVID-19, evaluate local respiratory immune responses to SARS-CoV-2 infection, and develop a prognostic tool for COVID-19 severity using accessible early indicators. Using nasopharyngeal swab samples from hospitalized patients with COVID-19 of varying severity during the first wave of the pandemic from March to May 2020 in Louisiana, we evaluated the association between COVID-19 severity and viral load, respiratory immune mediators, and demographic/clinical factors. We found that the SpO2/FiO2 ratio at triage, total comorbidity burden (represented by Charlson Comorbidity Index), and gender were significantly associated with COVID-19 severity. Using these early significant indicators, we developed a prognostic tool for COVID-19 severity that is simple and convenient. Additionally, our study demonstrated that elevated levels of respiratory immune mediators, including IL-10, IL-6, MCP-1, and MCP-3, were significantly associated with COVID-19 severity. We also found that viral load at the time of admission was associated with disease severity. Our findings highlight the feasibility and importance of evaluating the humoral component of local mucosal immune responses and viral load at the infected site using convenient nasopharyngeal swab samples, which could be an effective method to understand the relationship between viral infection and immune responses at the early stages of infection. Our proposed prognostic tool has the potential to be useful for COVID-19 management in clinical settings, as it utilizes accessible and easy-to-collect variables at the time of admission.

Ensemble modeling of SARS-CoV-2 immune dynamics in immunologically naïve rhesus macaques predicts that potent, early innate immune responses drive viral elimination

Introduction

An unprecedented breadth of longitudinal viral and multi-scale immunological data has been gathered during SARS-CoV-2 infection. However, due to the high complexity, non-linearity, multi-dimensionality, mixed anatomic sampling, and possible autocorrelation of available immune data, it is challenging to identify the components of the innate and adaptive immune response that drive viral elimination. Novel mathematical models and analytical approaches are required to synthesize contemporaneously gathered cytokine, transcriptomic, flow cytometry, antibody response, and viral load data into a coherent story of viral control, and ultimately to discriminate drivers of mild versus severe infection.

Methods

We investigated a dataset describing innate, SARS-CoV-2 specific T cell, and antibody responses in the lung during early and late stages of infection in immunologically naïve rhesus macaques. We used multi-model inference and ensemble modeling approaches from ecology and weather forecasting to compare and combine various competing models.

Results and discussion

Model outputs suggest that the innate immune response plays a crucial role in controlling early infection, while SARS-CoV-2 specific CD4+ T cells correspond to later viral elimination, and anti-spike IgG antibodies do not impact viral dynamics. Among the numerous genes potentially contributing to the innate response, we identified IFI27 as most closely linked to viral load decline. A 90% knockdown of the innate response from our validated model resulted in a ~10-fold increase in peak viral load during infection. Our approach provides a novel methodological framework for future analyses of similar complex, non-linear multi-component immunologic data sets.

Post-migration infection with SARS-CoV-2 in Venezuelan migrants: A laboratory-based epidemiological observational study

BACKGROUND

Since 2015, over 6 million Venezuelans migrated to Colombia and neighboring countries. While most people adhered to lockdown measures, migrants kept moving during the COVID-19 pandemic.

METHOD

To investigate the extent of migration-associated SARS-CoV-2 infections, we interviewed 1209 adult Venezuelan migrants upon arrival to Bucaramanga, Colombia, 200 km from the Colombian-Venezuelan border along the main migration route during April-September 2021, collected individual-level socio-economic and clinical data, sampled blood and saliva, and assessed SARS-CoV-2 infection by serological, molecular and phylogenetic tools.

RESULTS

SARS-CoV-2 RT-PCR positivity was 1.9 % (95 % Confidence Interval (CI), 1.2-2.9) without varying significantly over the study period (chi-square, p = 0.922) and significantly associated with stay in Colombia >14 days (p = 0.018; prevalence ratio 3.3, 95 % CI, 1.2-8.7). Pre-existing SARS-CoV-2-specific antibodies were neither significantly associated with preventing infection (Chi-square, p = 0.188), nor symptom development (Fisher, p = 0.246). Predominance and time of detection of SARS-CoV-2 Mu and Gamma variants in migrants in comparison to available genomic data suggested infection predominantly in Colombia. SARS-CoV-2 IgG-based seroprevalence was 34.2 % (95 % CI, 31.5-36.9). Detection of SARS-CoV-2-specific antibodies was significantly associated with previous contact with infected individuals (p = 0.002).

CONCLUSIONS

SARS-CoV-2 infection occurred predominantly after immigration, potentially facilitated by densely populated border camps. Improved infrastructure and health care will prevent migration-associated spread of COVID-19 and other infectious diseases.

Nanoscale-localized multiplexed biological activation of field effect transistors for biosensing applications

The rise in antibiotic-resistant pathogens, highly infectious viruses, and chronic diseases has prompted the search for rapid and versatile medical tests that can be performed by the patient. Field-effect transistor (FET)-based electronic biosensing platforms are particularly attractive due to their sensitivity, fast turn-around time, potential for parallel detection of multiple pathogens, and compatibility with semiconductor manufacturing. However, an unmet critical need is a scalable, site-selective multiplexed biofunctionalization method with nanoscale precision for immobilizing different types of pathogen-specific bioreceptors on individual FETs, preventing parallel detection of multiple targets. Here, we propose a paradigm shift in FET biofunctionalization using thermal scanning probe lithography (tSPL) with a thermochemically sensitive polymer. This polymer can be spin-coated on fully-fabricated FET chips, making this approach applicable to any FET sensor material and technology. Crucially, we demonstrate the spatially selective multiplexed functionalization capability of this method by immobilizing different types of bioreceptors at prescribed locations on a chip with sub-20 nm resolution, paving the way for massively parallel FET detection of multiple pathogens. Antibody- and aptamer-modified graphene FET sensors are then realized, achieving ultra-sensitive detection of a minimum measured concentrations of 3 aM of SARS-CoV-2 spike proteins and 10 human SARS-CoV-2 infectious live virus particles per ml, and selectivity against human influenza A (H1N1) live virus.

Key performance evaluation of commercialized multiplex rRT-PCR kits for respiratory viruses: implications for application and optimization

Respiratory tract infections (RTIs) caused by viruses are prevalent and significant conditions in clinical settings. Accurate and effective detection is of paramount importance in the diagnosis, treatment, and prevention of viral RTIs. With technological advancements, multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assays have been developed and extensively adopted for the diagnosis of viral RTIs. Given the potential challenges in the detection performance of multiplex assays, this study evaluated the analytical sensitivity and competitive interference of the six most commonly used multiplex rRT-PCR kits for detection of respiratory viruses in China. The results revealed that the limits of detection were variable across the viruses and kits. Most of the evaluated multiplex kits demonstrated comparable or enhanced analytical sensitivity compared with singleplex kits for clinically significant viruses, including human adenovirus (HAdV)-3, HAdV-7, Omicron BA.5, H1N1pdm09, H3N2, B/Victoria, respiratory syncytial virus subtype A, and respiratory syncytial virus subtype B, whereas multiplex kits showed relatively less analytical sensitivity for human rhinovirus-B72, human metapneumovirus-A2, parainfluenza virus (PIV)-1, and PIV-3. In addition, most multiplex kits successfully identified co-infections when one analyte was present at a low concentration and another analyte was present at a high concentration.

IMPORTANCE

The complexity and severity of viral respiratory tract infections (RTIs) emphasize the pivotal role of precise diagnosis for viral RTIs in guiding effective public health responses and ensuring appropriate medical interventions, given the substantial population at risk. This study highlights the necessity and importance of evaluating the analytical validity of multiplex real-time reverse transcription polymerase chain reaction assays, offering valuable insights into their optimization and application.

COVID-19 severity and corticosteroid treatment have minimal effect on specific antibody production

BACKGROUND

Dexamethasone is currently administered for Coronavirus disease 2019(COVID-19); however, there are concerns about its effect on specific antibodies' production. The aim of this study was to evaluate whether specific antibodies were affected by COVID-19 severity and corticosteroid treatment.

METHODS

Of 251 confirmed COVID-19 patients admitted to our hospital between January 26 and August 10, 2020, the early period of the pandemic, 75 patients with sera within 1 month of onset and 1 month or longer were included in the research. A total of 253 serum samples from these patients were collected. The levels of specific antibodies for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2), immunoglobulin G (IgG) and M (IgM), were measured retrospectively. The results were compared separately of each COVID-19 severity, and with or without corticosteroid treatment.

RESULTS

Among the 75 patients, 47, 18, and 10 had mild, moderate, and severe disease, respectively. The median age was 53.0 years and 22 (29%) were women. The most common comorbidities were hypertension and dyslipidemia. Corticosteroids were administered to 20 (27%) and 10 (53%), patients with moderate and severe disease, respectively. The positivity rates IgM increased first, and IgG was almost always positive after day 16, regardless of the severity of COVID-19. On days 6-10, both IgG and IgM positivity rates were higher in patients with moderate disease than in those with mild or severe disease. In patients with moderate disease, IgG positivity was similar over time, regardless of corticosteroid treatment.

CONCLUSIONS

In COVID-19 patients, specific IgG is positive and maintained for a long period of time, even after corticosteroid treatment. The effect of corticosteroid treatment in a COVID-19 epidemiological study using specific IgG antibodies was considered minor. COVID-19 patients were more likely to receive oxygen if IgM was positive 1 week after onset, but not mechanical ventilation. IgM measurement 1 week after onset may predict COVID-19 severity.

Rapid and specific detection of nanoparticles and viruses one at a time using microfluidic laminar flow and confocal fluorescence microscopy

Mainstream virus detection relies on the specific amplification of nucleic acids via polymerase chain reaction, a process that is slow and requires extensive laboratory expertise and equipment. Other modalities, such as antigen-based tests, allow much faster virus detection but have reduced sensitivity. In this study, we introduce an approach for rapid and specific detection of single nanoparticles using a confocal-based flow virometer. The combination of laminar flow in a microfluidic channel and correlated fluorescence signals emerging from both free dyes and fluorescently labeled primary antibodies provide insights into nanoparticle volumes and specificities. We evaluate and validate the assay using fluorescent beads and viruses, including SARS-CoV-2 with fluorescently labeled primary antibodies. Additionally, we demonstrate how hydrodynamic focusing enhances the assay sensitivity for detecting viruses at relevant loads. Based on our results, we envision the future use of this technology for clinically relevant bio-nanoparticles, supported by the implementation of the assay in a portable and user-friendly setup.

COVID-19 Related Tracheal Stenosis Requiring Tracheal Resection: A Case Series

OBJECTIVE

To characterize the preoperative and intraoperative findings of symptomatic tracheal stenosis associated with COVID-19 related respiratory failure requiring tracheal resection.

METHOD

We performed a retrospective review identifying all patients with a history of tracheal stenosis secondary to COVID-19 related respiratory failure who subsequently received a tracheal resection at our institution between January 2020 and June 2023. Clinical, radiological, pathological, and surgical characteristics were recorded to describe and characterize pre-operative and intraoperative findings associated with tracheal stenosis in the setting of a previous COVID-19 infection.

RESULTS

We retrospectively reviewed 11 patients with COVID-19 related tracheal stenosis that required open tracheal or cricotracheal resection. The mean age was 54.1. Patients were hospitalized for a mean of 49.5 days related to COVID-19 complications. Tracheotomy was completed in 10 patients (90.9%) during their initial hospitalization with COVID-19 related respiratory failure. Patients were intubated a mean of 18.6 days prior to tracheotomy completion. Ten patients (90.9%) underwent endoscopic operative interventions for their tracheal stenosis prior to open resection. Intraoperatively, the mean stenosis length was 3.33 cm. The mean tracheal resection length was 3.96 cm. Patients were hospitalized for a mean of 8.27 days post operatively with no significant post operative complications.

CONCLUSIONS

Symptomatic tracheal stenosis in the setting of prolonged intubation due to COVID-19 is an under-described etiology. This is one of the largest single institution retrospective reviews that identifies 11 patients with prolonged intubation who developed symptomatic tracheal stenosis refractory to conservative management and ultimately requiring tracheal resection.

Universal Identification of Pathogenic Viruses by Liquid Chromatography Coupled with Tandem Mass Spectrometry Proteotyping

Accurate and rapid identification of viruses is crucial for an effective medical diagnosis when dealing with infections. Conventional methods, including DNA amplification techniques or lateral-flow assays, are constrained to a specific set of targets to search for. In this study, we introduce a novel tandem mass spectrometry proteotyping-based method that offers a universal approach for the identification of pathogenic viruses and other components, eliminating the need for a priori knowledge of the sample composition. Our protocol relies on a time and cost-efficient peptide sample preparation, followed by an analysis with liquid chromatography coupled to high-resolution tandem mass spectrometry. As a proof of concept, we first assessed our method on publicly available shotgun proteomics datasets obtained from virus preparations and fecal samples of infected individuals. Successful virus identification was achieved with 53 public datasets, spanning 23 distinct viral species. Furthermore, we illustrated the method's capability to discriminate closely related viruses within the same sample, using alphaviruses as an example. The clinical applicability of our method was demonstrated by the accurate detection of the vaccinia virus in spiked saliva, a matrix of paramount clinical significance due to its non-invasive and easily obtainable nature. This innovative approach represents a significant advancement in pathogen detection and paves the way for enhanced diagnostic capabilities.

Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis

Joint pain and osteoarthritis can occur as coronavirus disease 2019 (COVID-19) sequelae after infection. However, little is known about the damage to articular cartilage. Here we illustrate knee joint damage after wild-type, Delta and Omicron variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in vivo. Rapid joint injury with cystic lesions at the osteochondral junction was observed in two patients with post-COVID osteoarthritis and recapitulated in a golden Syrian hamster model. SARS-CoV-2-activated endothelin-1 signalling increased vascular permeability and caused viral spike proteins leakage into the subchondral bone. Osteoclast activation, chondrocyte dropout and cyst formation were confirmed histologically. The US Food and Drug Administration-approved endothelin receptor antagonist, macitentan, mitigated cystic lesions and preserved chondrocyte number in the acute phase of viral infection in hamsters. Delayed macitentan treatment at post-acute infection phase alleviated chondrocyte senescence and restored subchondral bone loss. It is worth noting that it could also attenuate viral spike-induced joint pain. Our work suggests endothelin receptor blockade as a novel therapeutic strategy for post-COVID arthritis.

Exploring the relationship between cycle threshold values and oral manifestations in COVID-19: a comprehensive overview

OBJECTIVE

This cross-sectional study aimed to compare oral manifestations between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-positive and SARS-CoV-2-negative patients and to examine associations between oral symptoms, Ct values of E and N SARS-CoV-2 viral genes, and the implications of low Ct values indicating a high viral load, which is a predictive factor for the outcome of COVID-19.

METHODS

A total of 353 participating patients were aged ≥18 years with clinical manifestations of COVID-19 infection and tested for SARS-CoV-2 carriage at the medical center, by reverse transcriptase polymerase chain reaction (RT-PCR). All patients filled out an anonymous digital questionnaire regarding oral and general symptoms and overall medical health.  Results: A significant association was found between SARS-CoV-2 carriage and dry mouth, unpleasant taste and changes in taste (p < 0.001); for example, 37.4% of the 147 SARS-CoV-2- positive participants had a dry mouth, compared to 18.9% of the 206 SARS-CoV-2- negative participants. Oral blisters were experienced by patients with an E gene Ct value of 10-20 (50%) or 21-30 (50%) (p = 0.041). Bad breath, dry mouth, unpleasant taste and changes in taste were mostly present in participants whose Ct values of both E and N genes were between 21 and 30.  Conclusions: This study found significant associations between low Ct values of E and N SARS-CoV-2 viral genes and high viral load, indicating that Ct values can serve as predictive factors for COVID-19 outcomes. The findings suggest that while oral symptoms are present, the Ct values and associated high viral loads are more critical indicators of disease severity and prognosis.

Validation of Saliva as the Clinical Specimen Type for a University-Wide COVID-19 Surveillance Program

At the beginning of the COVID-19 pandemic, the Georgia Institute of Technology made the decision to keep the university doors open for on-campus attendance. To manage COVID-19 infection rates, internal resources were applied to develop and implement a mass asymptomatic surveillance program. The objective was to identify infections early for proper follow-on verification testing, contact tracing, and quarantine/isolation as needed. Program success depended on frequent and voluntary sample collection from over 40,000 students, faculty, and staff personnel. At that time, the nasopharyngeal (NP) swab, not saliva, was the main accepted sample type for COVID-19 testing. However, due to collection discomfort and the inability to be self-collected, the NP swab was not feasible for voluntary and frequent self-collection. Therefore, saliva was selected as the clinical sample type and validated. A saliva collection kit and a sample processing and analysis workflow were developed. The results of a clinical sample-type comparison study between co-collected and matched NP swabs and saliva samples showed 96.7% positive agreement and 100% negative agreement. During the Fall 2020 and Spring 2021 semesters, 319,988 samples were collected and tested. The program resulted in maintaining a low overall mean positivity rate of 0.78% and 0.54% for the Fall 2020 and Spring 2021 semesters, respectively. For this high-throughput asymptomatic COVID-19 screening application, saliva was an exceptionally good sample type.

SARS-CoV-2 spike protein induces the cytokine release syndrome by stimulating T cells to produce more IL-2

Introduction

Cytokine release syndrome (CRS) is one of the leading causes of mortality in patients with COVID-19 caused by the SARS-CoV-2 coronavirus. However, the mechanism of CRS induced by SARS-CoV-2 is vague.

Methods

Using spike protein combined with IL-2, IFN-γ, and TNF-α to stimulate human peripheral blood mononuclear cells (PBMCs) to secrete CRS-related cytokines, the content of cytokines in the supernatant was detected, and the effects of NK, T, and monocytes were analyzed.

Results

This study shows that dendritic cells loaded with spike protein of SARS-CoV-2 stimulate T cells to release much more interleukin-2 (IL-2,) which subsequently cooperates with spike protein to facilitate PBMCs to release IL-1β, IL-6, and IL-8. These effects are achieved via IL-2 stimulation of NK cells to release tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ), as well as T cells to release IFN-γ Mechanistically, IFN-γ and TNF-α enhance the transcription of CD40, and the interaction of CD40 and its ligand stabilizes the membrane expression of toll-like receptor 4 (TLR4) that serves as a receptor of spike protein on the surface of monocytes. As a result, there is a constant interaction between spike protein and TLR4, leading to continuous activation of nuclear factor-κ-gene binding (NF-κB). Furthermore, TNF-α also activates NF-κB signaling in monocytes, which further cooperates with IFN-γ and spike protein to modulate NF-κB-dependent transcription of CRS-related inflammatory cytokines.

Discussion

Targeting TNF-α/IFN-γ in combination with TLR4 may represent a promising therapeutic approach for alleviating CRS in individuals with COVID-19.

Oral SARS-CoV-2 host responses predict the early COVID-19 disease course

Oral fluids provide ready detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and host responses. This study sought to evaluate relationships between oral virus, oral and systemic anti-SARS-CoV-2-specific antibodies, and symptoms. Oral fluids (saliva/throat wash (saliva/TW)) and serum were collected from asymptomatic and symptomatic, nasopharyngeal (NP) SARS-CoV-2 RT-qPCR+ human participants (n = 45). SARS-CoV-2 RT-qPCR and N-antigen detection by immunoblot and lateral flow assay (LFA) were performed. RT-qPCR for subgenomic RNA (sgRNA) was sequence confirmed. SARS-CoV-2-anti-S protein RBD LFA and ELISA assessed IgM and IgG responses. Structural analysis identified host salivary molecules analogous to SARS-CoV-2-N-antigen. At time of enrollment (baseline, BL), LFA-detected N-antigen in 86% of TW and was immunoblot-confirmed. However, only 3/17 were saliva/TW qPCR+ . Sixty percent of saliva and 83% of TW demonstrated persistent N-antigen at 4 weeks. N-antigen LFA signal in three anti-spike sero-negative participants suggested potential cross-detection of 4 structurally analogous salivary RNA binding proteins (alignment 19-29aa, RMSD 1-1.5 Angstroms). At enrollment, symptomatic participants demonstrated replication-associated sgRNA junctions, were IgG+ (94%/100% in saliva/TW), and IgM+ (63%/54%). At 4 weeks, SARS-CoV-2 IgG (100%/83%) and IgM (80%/67%) persisted. Oral and serum IgG correlated 100% with NP+ PCR status. Cough and fatigue severity (p = 0.010 and 0.018 respectively), and presence of weakness, nausea, and composite upper respiratory symptoms (p = 0.037, 0.005, and 0.017, respectively) were negatively associated with saliva IgM but not TW or serum IgM. Throat wash IgM levels were higher in women compared to men, although the association did not reach statistical significance (median: 290 (female) versus 0.697, p = 0.056). Important to transmission and disease course, oral viral replication and persistence showed clear relationships with select symptoms and early oral IgM responses during early infection. N-antigen cross-reactivity may reflect mimicry of structurally analogous host proteins.

Detection of SARS-CoV-2 on the environmental surfaces and its implications for pandemic preparedness

Even though death due to COVID-19 is no longer a public health emergency, less virulent but highly transmissible forms of SARS-CoV-2 continue to spread in many countries leading to outbreaks and rise in hospitalizations in the affected regions. Lessons learned during the pandemic must be put into action to protect the world's population from another catastrophe like COVID-19. Novel approaches that were developed for tracking the spread of SARS-CoV-2 included analysis of wastewater, air samples, and various environmental surfaces. We conducted a study in Kuwait during the peak of COVID-19 pandemic to examine if SARS-CoV-2 could be detected in swabs taken from frequently touched environmental surfaces. We selected 12 Cooperative Society Stores-two from each governorate of Kuwait-for collection of surface samples. The Cooperative Society Stores are widely distributed across the whole country and cater to daily household needs including groceries and other essential items. These stores operated even during the "lockdown" imposed at the height of the pandemic. We collected swabs from high-touch surfaces including the handles of the shopping carts and freezers, the elevators, the keypads of the point-of-service terminals of cash counters, and the automated teller machines. All the surfaces tested showed a variable presence of SARS-CoV-2 by reverse transcriptase quantitative PCR, showing the validity of the proof-of-concept study. Monitoring of the presence of SARS-CoV-2 by surface sampling thus offers a cheap but effective means of environmental surveillance for coronaviruses. We therefore strongly recommend the addition of surface environmental sampling as a strategy for pandemic preparedness everywhere.

Personal characteristics and transmission dynamics associated with SARS-CoV-2 semi-quantitative PCR test results: an observational study from Belgium, 2021-2022

Introduction

Following harmonization efforts by the Belgian National Reference Center for SARS-CoV-2, semi-quantitative PCR test (SQ-PCR) results, used as a proxy for viral load, were routinely collected after performing RT-qPCR tests.

Methods

We investigated both the personal characteristics associated with SQ-PCR results and the transmission dynamics involving these results. We used person-level laboratory test data and contact tracing data collected in Belgium from March 2021 to February 2022. Personal characteristics (age, sex, vaccination, and laboratory-confirmed prior infection) and disease stage by date of symptom onset were analyzed in relation to SQ-PCR results using logistic regression. Vaccine effectiveness (VE) against a high viral load (≥107 copies/mL) was estimated from the adjusted probabilities. Contact tracing involves the mandatory testing of high-risk exposure contacts (HREC) after contact with an index case. Odds ratios for test positivity and high viral load in HREC were calculated based on the SQ-PCR result of the index case using logistic regression models adjusted for age, sex, immunity status (vaccination, laboratory-confirmed prior infection), variant (Alpha, Delta, Omicron), calendar time, and contact tracing covariates.

Results

We included 909,157 SQ-PCR results of COVID-19 cases, 379,640 PCR results from index cases, and 72,052 SQ-PCR results of HREC. High viral load was observed more frequently among recent cases, symptomatic cases, cases over 25 years of age, and those not recently vaccinated (>90 days). The vaccine effectiveness (VE) of the primary schedule in the first 30 days after vaccination was estimated at 47.3% (95%CI 40.8-53.2) during the Delta variant period. A high viral load in index cases was associated with an increased test positivity in HREC (OR 2.7, 95%CI 2.62-2.79) and, among those testing positive, an increased likelihood of a high viral load (OR 2.84, 95%CI 2.53-3.19).

ƩS COVID-19 is a rapid high throughput and sensitive one-step quadruplex real-time RT-PCR assay

Real-time reverse transcription polymerase chain reaction (RT-PCR), a standard method recommended for the diagnosis of coronavirus disease 2019 (COVID-19) requires 2-4 h to get the result. Although antigen test kit (ATK) is used for COVID-19 screening within 15-30 min, the drawback is its limited sensitivity. Hence, a rapid one-step quadruplex real-time RT-PCR assay: termed ƩS COVID-19 targeting ORF1ab, ORF3a, and N genes of SARS-CoV-2; and Avocado sunblotch viroid (ASBVd) as an internal control was developed. Based on strategies including designing high melting temperature primers with short amplicons, applying a fast ramp rate, minimizing hold time, and reducing the range between denaturation and annealing/extension temperatures; the assay could be accomplished within 25 min. The limit of detection of ORF1ab, ORF3a, and N genes were 1.835, 1.310, and 1 copy/reaction, respectively. Validation was performed in 205 combined nasopharyngeal and oropharyngeal swabs. The sensitivity, specificity, positive predictive value, and negative predictive value were 92.8%, 100%, 100%, and 97.1%, respectively with 96.7% accuracy. Cohen's Kappa was 0.93. The newly developed rapid real-time RT-PCR assay was highly sensitive, specific, and fast, making it suitable for use as an alternative method to support laboratory diagnosis of COVID-19 in outpatient and emergency departments.

Performance characteristics of "lollipop" swabs for the diagnosis of infection with SARS-CoV-2

BACKGROUND

Common biologic samples used to diagnose COVID-19 include nasopharyngeal, nasal, or oropharyngeal swabs, and salivary samples. The performance characteristics of a sucked "lollipop" swab to detect SARS-CoV-2 virus is assessed in four small sub-studies.

METHODS

In each sub-study, a flocked swab was sucked for 20 s and submitted for PCR detection of SARS-CoV-2 virus.

RESULTS

Across all studies, 52 of 69 (75.4%) COVID-19 positive participants had positive "lollipop" swabs. Twelve of the 17 COVID-19 positive participants with negative "lollipop" swabs had known corresponding cycle threshold values of >37 from their nasal/nasopharyngeal swabs, an indication of low viral load at time of sampling. In a paired samples sub-study, the sensitivity and specificity of the "lollipop" swabs were 100% and 98%.

CONCLUSIONS

"Lollipop" swabs performed satisfactorily especially in individuals with acute infection of COVID-19. "Lollipop" swabs are a simple method of sample collection for detecting SARS-CoV-2 virus and warrants additional consideration.

BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies

BACKGROUND AND OBJECTIVE

Proteome microarrays are one of the popular high-throughput screening methods for large-scale investigation of protein interactions in cells. These interactions can be measured on protein chips when coupled with fluorescence-labeled probes, helping indicate potential biomarkers or discover drugs. Several computational tools were developed to help analyze the protein chip results. However, existing tools fail to provide a user-friendly interface for biologists and present only one or two data analysis methods suitable for limited experimental designs, restricting the use cases.

METHODS

In order to facilitate the biomarker examination using protein chips, we implemented a user-friendly and comprehensive web tool called BAPCP (Biomarker Analysis tool for Protein Chip Platforms) in this research to deal with diverse chip data distributions.

RESULTS

BAPCP is well integrated with standard chip result files and includes 7 data normalization methods and 7 custom-designed quality control/differential analysis filters for biomarker extraction among experiment groups. Moreover, it can handle cost-efficient chip designs that repeat several blocks/samples within one single slide. Using experiments of the human coronavirus (HCoV) protein microarray and the E. coli proteome chip that helps study the immune response of Kawasaki disease as examples, we demonstrated that BAPCP can accelerate the time-consuming week-long manual biomarker identification process to merely 3 min.

CONCLUSIONS

The developed BAPCP tool provides substantial analysis support for protein interaction studies and conforms to the necessity of expanding computer usage and exchanging information in bioscience and medicine. The web service of BAPCP is available at https://cosbi.ee.ncku.edu.tw/BAPCP/.

The significance of recurrent de novo amino acid substitutions that emerged during chronic SARS-CoV-2 infection: an observational study

BACKGROUND

De novo amino acid substitutions (DNS) frequently emerge among immunocompromised patients with chronic SARS-CoV-2 infection. While previous studies have reported these DNS, their significance has not been systematically studied.

METHODS

We performed a review of DNS that emerged during chronic SARS-CoV-2 infection. We searched PubMed until June 2023 using the keywords "(SARS-CoV-2 or COVID-19) and (mutation or sequencing) and ((prolonged infection) or (chronic infection) or (long term))". We included patients with chronic SARS-CoV-2 infection who had SARS-CoV-2 sequencing performed for at least 3 time points over at least 60 days. We also included 4 additional SARS-CoV-2 patients with chronic infection of our hospital not reported previously. We determined recurrent DNS that has appeared in multiple patients and determined the significance of these mutations among epidemiologically-significant variants.

FINDINGS

A total of 34 cases were analyzed, including 30 that were published previously and 4 from our hospital. Twenty two DNS appeared in ≥3 patients, with 14 (64%) belonging to lineage-defining mutations (LDMs) of epidemiologically-significant variants and 10 (45%) emerging among chronically-infected patients before the appearance of the corresponding variant. Notably, nsp9-T35I substitution (Orf1a T4175I) emerged in all three patients with BA.2.2 infection in 2022 before the appearance of Variants of Interest that carry nsp9-T35I as LDM (EG.5 and BA.2.86/JN.1). Structural analysis suggests that nsp9-T35I substitution may affect nsp9-nsp12 interaction, which could be critical for the function of the replication and transcription complex.

INTERPRETATION

DNS that emerges recurrently in different chronically-infected patients may be used as a marker for potential epidemiologically-significant variants.

FUNDING

Theme-Based Research Scheme [T11/709/21-N] of the Research Grants Council (See acknowledgements for full list).

Unravelling the diagnostic methodologies for SARS-CoV-2; the Indispensable need for developing point-of-care testing

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic that continues to be a global menace and since its emergence in the late 2019, SARS-CoV-2 has been vigorously spreading throughout the globe putting the whole world into a multidimensional calamity. The suitable diagnosis strategies are on the front line of the battle against preventing the spread of infections. Since the clinical manifestation of COVID-19 is shared between various diseases, detection of the unique impacts of the pathogen on the host along with the diagnosis of the virus itself should be addressed. Employing the most suitable approaches to specifically, sensitively and effectively recognize the infected cases may be a real game changer in controlling the outbreak and the crisis management. In that matter, point-of-care assays (POC) appears to be the potential option, due to sensitivity, specificity, affordable, and availability. Here we brief the most recent findings about the virus, its variants, and the conventional methods that have been used for its detection, along with the POC strategies that have been applied to the virus diagnosis and the developing technologies which can accelerate the diagnosis procedure yet maintain its efficiency.

Vitamin D supplementation and calcium: Many-faced gods or nobody in fighting against Corona Virus Disease 2019

In December 2019, Corona Virus Disease 2019 (COVID-19) was first identified and designated as a pandemic in March 2020 due to rapid spread of the virus globally. At the beginning of the pandemic, only a few treatment options, mainly focused on supportive care and repurposing medications, were available. Due to its effects on immune system, vitamin D was a topic of interest during the pandemic, and researchers investigated its potential impact on COVID-19 outcomes. However, the results of studies about the impact of vitamin D on the disease are inconclusive. In the present narrative review, different roles of vitamin D regarding the COVID-19 have been discussed to show that vitamin D supplementation should be recommended carefully.

Development of a Diagnostic Microfluidic Chip for SARS-CoV-2 Detection in Saliva and Nasopharyngeal Samples

The novel coronavirus SARS-CoV-2 was first isolated in late 2019; it has spread to all continents, infected over 700 million people, and caused over 7 million deaths worldwide to date. The high transmissibility of the virus and the emergence of novel strains with altered pathogenicity and potential resistance to therapeutics and vaccines are major challenges in the study and treatment of the virus. Ongoing screening efforts aim to identify new cases to monitor the spread of the virus and help determine the danger connected to the emergence of new variants. Given its sensitivity and specificity, nucleic acid amplification tests (NAATs) such as RT-qPCR are the gold standard for SARS-CoV-2 detection. However, due to high costs, complexity, and unavailability in low-resource and point-of-care (POC) settings, the available RT-qPCR assays cannot match global testing demands. An alternative NAAT, RT-LAMP-based SARS-CoV-2 detection offers scalable, low-cost, and rapid testing capabilities. We have developed an automated RT-LAMP-based microfluidic chip that combines the RNA isolation, purification, and amplification steps on the same device and enables the visual detection of SARS-CoV-2 within 40 min from saliva and nasopharyngeal samples. The entire assay is executed inside a uniquely designed, inexpensive disposable microfluidic chip, where assay components and reagents have been optimized to provide precise and qualitative results and can be effectively deployed in POC settings. Furthermore, this technology could be easily adapted for other novel emerging viruses.

ACE2-Decorated Virus-Like Particles Effectively Block SARS-CoV-2 Infection

Purpose

Over the past three years, extensive research has been dedicated to understanding and combating COVID-19. Targeting the interaction between the SARS-CoV-2 Spike protein and the ACE2 receptor has emerged as a promising therapeutic strategy against SARS-CoV-2. This study aimed to develop ACE2-coated virus-like particles (ACE2-VLPs), which can be utilized to prevent viral entry into host cells and efficiently neutralize the virus.

Methods

Virus-like particles were generated through the utilization of a packaging plasmid in conjunction with a plasmid containing the ACE2 envelope sequence. Subsequently, ACE2-VLPs and ACE2-EVs were purified via ultracentrifugation. The quantification of VLPs was validated through multiple methods, including Nanosight 3000, TEM imaging, and Western blot analysis. Various packaging systems were explored to optimize the ACE2-VLP configuration for enhanced neutralization capabilities. The evaluation of neutralization effectiveness was conducted using pseudoviruses bearing different spike protein variants. Furthermore, the study assessed the neutralization potential against the Omicron BA.1 variant in Vero E6 cells.

Results

ACE2-VLPs showed a high neutralization capacity even at low doses and demonstrated superior efficacy in in vitro pseudoviral assays compared to extracellular vesicles carrying ACE2. ACE2-VLPs remained stable under various environmental temperatures and effectively blocked all tested variants of concern in vitro. Notably, they exhibited significant neutralization against Omicron BA.1 variant in Vero E6 cells. Given their superior efficacy compared to extracellular vesicles and proven success against live virus, ACE2-VLPs stand out as crucial candidates for treating SARS-CoV-2 infections.

Conclusion

This novel therapeutic approach of coating VLPs with receptor particles provides a proof-of-concept for designing effective neutralization strategies for other viral diseases in the future.

Risk Factors for Impaired Cellular or Humoral Immunity after Three Doses of SARS-CoV-2 Vaccine in Healthy and Immunocompromised Individuals

Background: We aimed to identify the risk factors for impaired cellular and humoral immunity after three doses of the SARS-CoV-2 vaccine. Methods: Six months after the third vaccine dose, T-cell immunity was evaluated using interferon-gamma release assays (IGRAs) in 60 healthy and 139 immunocompromised (IC) individuals, including patients with hematologic malignancy (HM), solid malignancy (SM), rheumatic disease (RD), and kidney transplantation (KT). Neutralizing antibody titers were measured using the plaque reduction neutralization test (PRNT) and surrogate virus neutralization test (sVNT). Results: T-cell immunity results showed that the percentages of IGRA-positive results using wild-type/alpha spike protein (SP) and beta/gamma SP were 85% (51/60) and 75% (45/60), respectively, in healthy individuals and 45.6% (62/136) and 40.4% (55/136), respectively, in IC individuals. IC with SM or KT showed a high percentage of IGRA-negative results. The underlying disease poses a risk for impaired cellular immune response to wild-type SP. The risk was low when all doses were administered as mRNA vaccines. The risk factors for an impaired cellular immune response to beta/gamma SP were underlying disease and monocyte%. In the sVNT using wild-type SP, 12 of 191 (6.3%) individuals tested negative. In the PRNT of 46 random samples, 6 (13%) individuals tested negative for the wild-type virus, and 19 (41.3%) tested negative with omicrons. KT poses a risk for an impaired humoral immune response. Conclusions: Underlying disease poses a risk for impaired cellular immune response after the third dose of the SARS-CoV-2 vaccine; KT poses a risk for impaired humoral immune response, emphasizing the requirement of precautions in patients.

Omicron variant and pulmonary involvements: a chest imaging analysis in asymptomatic and mild COVID-19

Objectives

To identify clinical characteristics and risk factors for pulmonary involvements in asymptomatic and mildly symptomatic patients infected with SARS-CoV-2 Omicron variant by chest imaging analysis.

Methods

Detailed data and chest computed tomography (CT) imaging features were retrospectively analyzed from asymptomatic and mildly symptomatic patients infected with Omicron between 24 April and 10 May 2022. We scored chest CT imaging features and categorized the patients into obvious pulmonary involvements (OPI) (score > 2) and not obvious pulmonary involvements (NOPI) (score ≤ 2) groups based on the median score. The risk factors for OPI were identified with analysis results visualized by nomogram.

Results

In total, 339 patients were included (145 were male and 194 were female), and the most frequent clinical symptoms were cough (75.5%); chest CT imaging features were mostly linear opacities (42.8%). Pulmonary involvements were more likely to be found in the left lower lung lobe, with a significant difference in the lung total severity score of the individual lung lobes (p < 0.001). Logistic regression analysis revealed age stratification [odds ratio (OR) = 1.92, 95% confidence interval (CI) (1.548-2.383); p < 0.001], prolonged nucleic acid negative conversion time (NCT) (NCT > 8d) [OR = 1.842, 95% CI (1.104-3.073); p = 0.019], and pulmonary diseases [OR = 4.698, 95% CI (1.159-19.048); p = 0.03] as independent OPI risk factors.

Conclusion

Asymptomatic and mildly symptomatic patients infected with Omicron had pulmonary involvements which were not uncommon. Potential risk factors for age stratification, prolonged NCT, and pulmonary diseases can help clinicians to identify OPI in asymptomatic and mildly symptomatic patients infected with Omicron.

Optical detection of infectious SARS-CoV-2 virions by counting spikes

Existing methods for the mass detection of viruses are limited to the registration of small amounts of a viral genome or specific protein markers. In spite of high sensitivity, the applied methods cannot distinguish between virulent viral particles and non-infectious viral particle debris. We report an approach to solve this long-standing challenge using the SARS-CoV-2 virus as an example. We show that wide-field optical microscopy with the state-of-the-art mesoscopic fluorescent labels, formed by a core-shell plasmonic nanoparticle with fluorescent dye molecules in the core-shell that are strongly coupled to the plasmonic nanoparticle, not only rapidly, i.e. in less than 20 minutes after sampling, detects SARS-CoV-2 virions directly in a patient sample without a pre-concentration step, but can also distinguish between infectious and non-infectious virus strains by counting the spikes on the lipid envelope of individual viral particles.

Symptom propagation in respiratory pathogens of public health concern: a review of the evidence

Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clusters of severe disease. Conversely, it could result in chains of mild infection, generating widespread immunity with minimal cost to public health. Despite accumulating evidence that symptom propagation occurs for many respiratory pathogens, the underlying mechanisms are not well understood. Here, we conducted a scoping literature review for 14 respiratory pathogens to ascertain the extent of evidence for symptom propagation by two mechanisms: dose-severity relationships and route-severity relationships. We identify considerable heterogeneity between pathogens in the relative importance of the two mechanisms, highlighting the importance of pathogen-specific investigations. For almost all pathogens, including influenza and SARS-CoV-2, we found support for at least one of the two mechanisms. For some pathogens, including influenza, we found convincing evidence that both mechanisms contribute to symptom propagation. Furthermore, infectious disease models traditionally do not include symptom propagation. We summarize the present state of modelling advancements to address the methodological gap. We then investigate a simplified disease outbreak scenario, finding that under strong symptom propagation, isolating mildly infected individuals can have negative epidemiological implications.

Submandibular Gland Pathogenesis Following SARS-CoV-2 Infection and Implications for Xerostomia

Although SARS-CoV-2 induces mucin hypersecretion in the respiratory tract, hyposalivation/xerostomia has been reported by COVID-19 patients. We evaluate the submandibular gland (SMGs) pathogenesis in SARS-CoV-2-infected K18-hACE2 mice, focusing on the impact of infection on the mucin production and structural integrity of acini, ductal system, myoepithelial cells (MECs) and telocytes. The spike protein, the nucleocapsid protein, hACE2, actin, EGF, TNF-α and IL-1β were detected by immunofluorescence, and the Egfr and Muc5b expression was evaluated. In the infected animals, significant acinar hypertrophy was observed in contrast to ductal atrophy. Nucleocapsid proteins and/or viral particles were detected in the SMG cells, mainly in the nuclear membrane-derived vesicles, confirming the nuclear role in the viral formation. The acinar cells showed intense TNF-α and IL-1β immunoexpression, and the EGF-EGFR signaling increased, together with Muc5b upregulation. This finding explains mucin hypersecretion and acinar hypertrophy, which compress the ducts. Dying MECs and actin reduction were also observed, indicating failure of contraction and acinar support, favoring acinar hypertrophy. Viral assembly was found in the dying telocytes, pointing to these intercommunicating cells as viral transmitters in SMGs. Therefore, EGF-EGFR-induced mucin hypersecretion was triggered by SARS-CoV-2 in acinar cells, likely mediated by cytokines. The damage to telocytes and MECs may have favored the acinar hypertrophy, leading to ductal obstruction, explaining xerostomia in COVID-19 patients. Thus, acinar cells, telocytes and MECs may be viral targets, which favor replication and cell-to-cell viral transmission in the SMG, corroborating the high viral load in saliva of infected individuals.

Determinants of Systemic SARS-CoV-2-Specific Antibody Responses to Infection and to Vaccination: A Secondary Analysis of Randomised Controlled Trial Data

SARS-CoV-2 infections elicit antibodies against the viral spike (S) and nucleocapsid (N) proteins; COVID-19 vaccines against the S-protein only. The BCG-Corona trial, initiated in March 2020 in SARS-CoV-2-naïve Dutch healthcare workers, captured several epidemic peaks and the introduction of COVID-19 vaccines during the one-year follow-up. We assessed determinants of systemic anti-S1 and anti-N immunoglobulin type G (IgG) responses using trial data. Participants were randomised to BCG or placebo vaccination, reported daily symptoms, SARS-CoV-2 test results, and COVID-19 vaccinations, and donated blood for SARS-CoV-2 serology at two time points. In the 970 participants, anti-S1 geometric mean antibody concentrations (GMCs) were much higher than anti-N GMCs. Anti-S1 GMCs significantly increased with increasing number of immune events (SARS-CoV-2 infection or COVID-19 vaccination): 104.7 international units (IU)/mL, 955.0 IU/mL, and 2290.9 IU/mL for one, two, and three immune events, respectively (p < 0.001). In adjusted multivariable linear regression models, anti-S1 and anti-N log10 concentrations were significantly associated with infection severity, and anti-S1 log10 concentration with COVID-19 vaccine type/dose. In univariable models, anti-N log10 concentration was also significantly associated with acute infection duration, and severity and duration of individual symptoms. Antibody concentrations were not associated with long COVID or long-term loss of smell/taste.