The effects of probiotic Lactobacillus acidophilus and colchicine on the control of symptoms, duration, and disease progression of mild and moderate cases of COVID-19: A randomized controlled clinical trial (preprint)

Background Coronavirus disease 2019 (COVID-19) is a newly emerging human disease caused by a novel coronavirus, causing a global pandemic crisis. Probiotics and/or colchicine may be considered as options for treatment since they have anti-viral, anti-inflammatory, and immunomodulatory effects.Objective To assess the effectiveness of probiotic supplements (Lactobacillus acidophilus) and colchicine on symptoms, duration, and progression of mild and moderate cases of COVID-19 infection.Methods A three-arm randomized controlled clinical trial was carried out in the triage clinic of the family medicine department at Ain Shams University Hospitals on 150 participants who had been diagnosed as COVID-19 patients with mild and moderate severity. Patients aged below 18 years or above 65 years with any co-morbidities, pregnant or lactating females, and severe COVID-19 confirmed cases were excluded. Randomization was done by using sealed envelopes containing codes for intervention or control. Patients are followed up for improvement of their symptoms with no development of new symptoms over the course of two weeks.Results A total of 150 patients with mild and moderate severity of COVID-19 were enrolled in the study, 50 patients in each arm; around one third (34.7%) of the participants were aged between 29 and 39 years; one-quarter (24.7%) were aged between 18 and 28 years and 40.6% were aged 40 years and above. The mean duration of symptoms improvement was 12, 11 and 12 in the colchicine, probiotic, and control groups, respectively. Improvement of inflammatory markers over time occurred in each of the three groups, with no statistically significant difference between them.Conclusion Probiotic Lactobacillus acidophilus and colchicine shows no significant effect on the symptoms, duration, and progression of mild and moderate cases of COVID-19.

Long-term persistence of RBD+ memory B cells encoding neutralizing antibodies in SARS-CoV-2 infection.

Considerable concerns relating to the duration of protective immunity against severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) exist, with evidence of antibody titers declining rapidly after infection and reports of reinfection. Here, we monitor the antibody responses against SARS-CoV-2 receptor-binding domain (RBD) for up to 6 months after infection. While antibody titers are maintained, ∼13% of the cohort's neutralizing responses return to background. However, encouragingly, in a selected subset of 13 participants, 12 have detectable RBD-specific memory B cells and these generally are increasing out to 6 months. Furthermore, we are able to generate monoclonal antibodies with SARS-CoV-2 neutralizing capacity from these memory B cells. Overall, our study suggests that the loss of neutralizing antibodies in plasma may be countered by the maintenance of neutralizing capacity in the memory B cell repertoire.

The Coronavirus Disease 2019 Rebound Study: A Prospective Cohort Study to Evaluate Viral and Symptom Rebound Differences in Participants Treated With Nirmatrelvir Plus Ritonavir Versus Untreated Controls.

BACKGROUND: The uptake of nirmatrelvir plus ritonavir (NPR) in patients with coronavirus disease 2019 (COVID-19) has been limited by concerns around the rebound phenomenon despite the scarcity of evidence around its epidemiology. The purpose of this study was to prospectively compare the epidemiology of rebound in NPR-treated and untreated participants with acute COVID-19 infection. METHODS: We designed a prospective, observational study in which participants who tested positive for COVID-19 and were clinically eligible for NPR were recruited to be evaluated for either viral or symptom clearance and rebound. Participants were assigned to the treatment or control group based on their decision to take NPR. Following initial diagnosis, both groups were provided 12 rapid antigen tests and asked to test on a regular schedule for 16 days and answer symptom surveys. Viral rebound based on test results and COVID-19 symptom rebound based on patient-reported symptoms were evaluated. RESULTS: Viral rebound incidence was 14.2% in the NPR treatment group (n = 127) and 9.3% in the control group (n = 43). Symptom rebound incidence was higher in the treatment group (18.9%) compared to controls (7.0%). There were no notable differences in viral rebound by age, gender, preexisting conditions, or major symptom groups during the acute phase or at the 1-month interval. CONCLUSIONS: This preliminary report suggests that rebound after clearance of test positivity or symptom resolution is higher than previously reported. However, notably we observed a similar rate of rebound in both the NPR treatment and control groups. Large studies with diverse participants and extended follow-up are needed to better understand the rebound phenomena.

High activation levels maintained in receptor-binding domain-specific memory B cells in people with severe coronavirus disease 2019.

The long-term health consequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are still being understood. The molecular and phenotypic properties of SARS-CoV-2 antigen-specific T cells suggest a dysfunctional profile that persists in convalescence in those who were severely ill. By contrast, the antigen-specific memory B-cell (MBC) population has not yet been analyzed to the same degree, but phenotypic analysis suggests differences following recovery from mild or severe coronavirus disease 2019 (COVID-19). Here, we performed single-cell molecular analysis of the SARS-CoV-2 receptor-binding domain (RBD)-specific MBC population in three patients after severe COVID-19 and four patients after mild/moderate COVID-19. We analyzed the transcriptomic and B-cell receptor repertoire profiles at ~2 months and ~4 months after symptom onset. Transcriptomic analysis revealed a higher level of tumor necrosis factor-alpha (TNF-α) signaling via nuclear factor-kappa B in the severe group, involving CD80, FOS, CD83 and TNFAIP3 genes that was maintained over time. We demonstrated the presence of two distinct activated MBCs subsets based on expression of CD80hi TNFAIP3hi and CD11chi CD95hi at the transcriptome level. Both groups revealed an increase in somatic hypermutation over time, indicating progressive evolution of humoral memory. This study revealed distinct molecular signatures of long-term RBD-specific MBCs in convalescence, indicating that the longevity of these cells may differ depending on acute COVID-19 severity.

Longitudinal Characterization of Phagocytic and Neutralization Functions of Anti-Spike Antibodies in Plasma of Patients after Severe Acute Respiratory Syndrome Coronavirus 2 Infection.

Phagocytic responses by effector cells to opsonized viruses have been recognized to play a key role in antiviral immunity. Limited data on coronavirus disease 2019 suggest that the role of Ab-dependent and -independent phagocytosis may contribute to the observed immunological and inflammatory responses; however, their development, duration, and role remain to be fully elucidated. In this study of 62 acute and convalescent patients, we found that patients with acute coronavirus disease 2019 can mount a phagocytic response to autologous plasma-opsonized Spike protein-coated microbeads as early as 10 d after symptom onset, while heat inactivation of this plasma caused 77-95% abrogation of the phagocytic response and preblocking of Fc receptors showed variable 18-60% inhibition. In convalescent patients, phagocytic response significantly correlated with anti-Spike IgG titers and older patients, while patients with severe disease had significantly higher phagocytosis and neutralization functions compared with patients with asymptomatic, mild, or moderate disease. A longitudinal subset of the convalescent patients over 12 mo showed an increase in plasma Ab affinity toward Spike Ag and preservation of phagocytic and neutralization functions, despite a decline in the anti-Spike IgG titers by >90%. Our data suggest that early phagocytosis is primarily driven by heat-liable components of the plasma, such as activated complements, while anti-Spike IgG titers account for the majority of observed phagocytosis at convalescence. Longitudinally, a significant increase in the affinity of the anti-Spike Abs was observed that correlated with the maintenance of both the phagocytic and neutralization functions, suggesting an improvement in the quality of the Abs.

Recalibrating SARS-CoV-2 Antigen Rapid Lateral Flow Test Relative Sensitivity from Validation Studies to Absolute Sensitivity for Indicating Individuals Shedding Transmissible Virus.

Testing for SARS-CoV-2 internationally has focused on COVID-19 diagnosis among symptomatic individuals using reverse transcriptase polymerase chain reaction (PCR) tests. Recently, however, SARS-CoV-2 antigen rapid lateral flow tests (LFT) have been rolled out in several countries for testing asymptomatic individuals in public health programmes. Validation studies for LFT have been largely cross-sectional, reporting sensitivity, specificity and predictive values of LFT relative to PCR. However, because PCR detects genetic material left behind for a long period when the individual is no longer infectious, these statistics can under-represent the sensitivity of LFT for detecting infectious individuals, especially when sampling asymptomatic populations. LFTs (intended to detect individuals shedding SARS-CoV-2 antigens) validated against PCR (intended to diagnose infection) are not reporting against a gold standard of equivalent measurements. Instead, these validation studies have reported relative performance statistics that need recalibrating to the purpose for which LFT is being used. We present an approach to this recalibration. We derive a formula for recalibrating relative performance statistics from LFT vs PCR validation studies to give likely absolute sensitivity of LFT for detecting individuals who are shedding shedding SARS-CoV-2 antigens. We contrast widely reported apparent sensitivities of LFT with recalibrated absolute sensitivity for detecting individuals shedding SARS-CoV-2 antigens. After accounting for within-individual viral kinetics and epidemic dynamics within asymptomatic populations we show that a highly performant test for SARS-CoV-2 antigen should show LFT-to-PCR relative sensitivity of less than 50% in conventional validation studies, which after re-calibration would be an absolute sensitivity of more than 80%. Further studies are needed to ascertain the absolute sensitivity of LFT as a test of infectiousness in COVID-19 responses. These studies should include longitudinal series of LFT and PCR, ideally in cohorts sampled from both contacts of cases and the general population.

Real World Performance of SARS-CoV-2 Antigen Rapid Diagnostic Tests in Various Clinical Settings.

OBJECTIVE: To assess the validity of Antigen rapid diagnostic tests (Ag-RDT) for SARS-CoV-2 as decision support tool in various hospital-based clinical settings. DESIGN: Retrospective cohort study among symptomatic and asymptomatic patients and Healthcare workers (HCW). SETTING: A large tertiary teaching medical center serving as a major COVID-19 hospitalizing facility. PARTICIPANTS AND METHODS: Ag-RDTs' performance was assessed in three clinical settings: 1. Symptomatic patients and HCW presenting at the Emergency Departments 2. Asymptomatic patients screened upon hospitalization 3. HCW of all sectors tested at the HCW clinic following exposure. RESULTS: We obtained 5172 samples from 4595 individuals, who had both Ag-RDT and quantitative real-time PCR (qRT-PCR) results available. Of these, 485 samples were positive by qRT-PCR. The positive percent agreement (PPA) of Ag-RDT was greater for lower cycle threshold (Ct) values, reaching 93% in cases where Ct-value was <25 and 85% where Ct-value was <30. PPA was similar between symptomatic and asymptomatic individuals. We observed a significant correlation between Ct-value and time from infection onset (p<0.001). CONCLUSIONS: Ag-RDT are highly sensitive to the infectious stage of COVID-19 manifested by either high viral load (lower Ct) or proximity to infection, whether patient is symptomatic or asymptomatic. Thus, this simple-to-use and inexpensive detection method can be used as a decision support tool in various in-hospital clinical settings, assisting patient flow and maintaining sufficient hospital staffing.

Mathematical Modeling to Inform Vaccination Strategies and Testing Approaches for Coronavirus Disease 2019 (COVID-19) in Nursing Homes.

BACKGROUND: Nursing home residents and staff were included in the first phase of coronavirus disease 2019 vaccination in the United States. Because the primary trial endpoint was vaccine efficacy (VE) against symptomatic disease, there are limited data on the extent to which vaccines protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the ability to infect others (infectiousness). Assumptions about VE against infection and infectiousness have implications for changes to infection prevention guidance for vaccinated populations, including testing strategies. METHODS: We use a stochastic agent-based Susceptible-Exposed-Infectious (Asymptomatic/Symptomatic)-Recovered model of a nursing home to simulate SARS-CoV-2 transmission. We model 3 scenarios, varying VE against infection, infectiousness, and symptoms, to understand the expected impact of vaccination in nursing homes, increasing staff vaccination coverage, and different screening testing strategies under each scenario. RESULTS: Increasing vaccination coverage in staff decreases total symptomatic cases in the nursing home (among staff and residents combined) in each VE scenario. In scenarios with 50% and 90% VE against infection and infectiousness, increasing staff coverage reduces symptomatic cases among residents. If vaccination only protects against symptoms, and asymptomatic cases remain infectious, increased staff coverage increases symptomatic cases among residents. However, this is outweighed by the reduction in symptomatic cases among staff. Higher frequency testing-more than once weekly-is needed to reduce total symptomatic cases if the vaccine has lower efficacy against infection and infectiousness, or only protects against symptoms. CONCLUSIONS: Encouraging staff vaccination is not only important for protecting staff, but might also reduce symptomatic cases in residents if a vaccine confers at least some protection against infection or infectiousness.

TIPICO XI: report of the first series and podcast on infectious diseases and vaccines (aTIPICO).

TIPiCO is an annual expert meeting and workshop on infectious diseases and vaccination. The edition of 2020 changed its name and format to aTIPiCO, the first series and podcasts on infectious diseases and vaccines. A total of 13 prestigious experts from different countries participated in this edition launched on the 26 November 2020. The state of the art of coronavirus disease-2019 (COVID-19) and the responsible pathogen, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and the options to tackle the pandemic situation were discussed in light of the knowledge in November 2020. Despite COVID-19, the status of other infectious diseases, including influenza infections, respiratory syncytial virus disease, human papillomavirus infection, measles, pertussis, tuberculosis, meningococcal disease, and pneumococcal disease, were also addressed. The essential lessons that can be learned from these diseases and their vaccines to use in the COVID-19 pandemic were also commented with the experts.

Reopening Scenarios

We use a five-age epidemiological model, combined with 66-sector economic accounting, to address a variety of questions concerning the economic reopening. We calibrate/estimate the model using contact survey data and data on weekly historical individual actions and non-pharmaceutical interventions in the weeks ending March 8 – May 16, 2020. Going forward, we model a decision-maker (governor) as following reopening guidelines like those proposed by the White House and the CDC. The sectoral accounting, combined with information on personal proximity and ability to work from home by sector, make it possible to construct a GDP-to-Risk index of which sectors provide the greatest increment in GDP per marginal increase in R0. Through simulations, we find that: a strong economic reopening is possible;a “smart” reopening, preferencing some sectors over others, makes only modest improvements over a broad reopening;and all this hinges on retaining strong restrictions on non-work social contacts. If non-work contacts – going to bars, shopping without social distancing and masks, large group gatherings, etc. – return only half-way to the pre-COVID-19 baseline, the current decline in deaths reverses leading to a second wave of business closures.

Economic Benefits of COVID-19 Screening Tests

We assess the economic value of screening testing programs as a policy response to the ongoing COVID-19 pandemic. We find that the fiscal, macroeconomic, and health benefits of rapid SARS-CoV-2 screening testing programs far exceed their costs, with the ratio of economic benefits to costs typically in the range of 4-15 (depending on program details), not counting the monetized value of lives saved. Unless the screening test is highly specific, however, the signal value of the screening test alone is low, leading to concerns about adherence. Confirmatory testing increases the net economic benefits of screening tests by reducing the number of healthy workers in quarantine and by increasing adherence to quarantine measures. The analysis is undertaken using a behavioral SIR model for the United States with 5 age groups, 66 economic sectors, screening and diagnostic testing, and partial adherence to instructions to quarantine or to isolate.

Development of at-home sample collection logistics for large-scale seroprevalence studies.

BACKGROUND: Serological studies rely on the recruitment of representative cohorts; however, such efforts are specially complicated by the conditions surrounding the COVID19 pandemic. METHODS: We aimed to design and implement a fully remote methodology for conducting safe serological surveys that also allow for the engagement of representative study populations. RESULTS: This design was well-received and effective. 2,066 participants ≥18 years old were enrolled, reflecting the ethnic and racial composition of Massachusetts. >70% of them reported being satisfied/extremely satisfied with the online enrollment and at-home self-collection of blood samples. While 18.6% reported some discomfort experienced with the collection process, 72.2% stated that they would be willing to test weekly if enrolled in a long-term study. CONCLUSIONS: High engagement and positive feedback from participants, as well as the quality of self-collected specimens, point to the usefulness of this fully remote, self-collection-based study design for future safer and efficient population-level serological surveys.

A Global lmmunological Observatory to meet a time of pandemics.

SARS-CoV-2 presents an unprecedented international challenge, but it will not be the last such threat. Here, we argue that the world needs to be much better prepared to rapidly detect, define and defeat future pandemics. We propose that a Global Immunological Observatory and associated developments in systems immunology, therapeutics and vaccine design should be at the heart of this enterprise.

Vaccine nationalism and the dynamics and control of SARS-CoV-2.

Vaccines provide powerful tools to mitigate the enormous public health and economic costs that the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to exert globally, yet vaccine distribution remains unequal among countries. To examine the potential epidemiological and evolutionary impacts of "vaccine nationalism," we extend previous models to include simple scenarios of stockpiling between two regions. In general, when vaccines are widely available and the immunity they confer is robust, sharing doses minimizes total cases across regions. A number of subtleties arise when the populations and transmission rates in each region differ, depending on evolutionary assumptions and vaccine availability. When the waning of natural immunity contributes most to evolutionary potential, sustained transmission in low-access regions results in an increased potential for antigenic evolution, which may result in the emergence of novel variants that affect epidemiological characteristics globally. Overall, our results stress the importance of rapid, equitable vaccine distribution for global control of the pandemic.

Cross-Sectional Assessment of SARS-CoV-2 Viral Load by Symptom Status in Massachusetts Congregate Living Facilities.

Transmission of coronavirus disease 2019 (COVID-19) from people without symptoms confounds societal mitigation strategies. From April to June 2020, we tested nasopharyngeal swabs by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) from 15 514 staff and 16 966 residents of nursing homes and assisted living facilities in Massachusetts. Cycle threshold (Ct) distributions were very similar between populations with (n = 739) and without (n = 2179) symptoms at the time of sampling (mean Ct, 25.7 vs 26.4; ranges 12-38). However, as local cases waned, those without symptoms shifted towards higher Ct. With such similar viral load distributions, existing testing modalities should perform comparably regardless of symptoms, contingent upon time since infection.

Immune age and biological age as determinants of vaccine responsiveness among elderly populations: the Human Immunomics Initiative research program.

The Human Immunomics Initiative (HII), a joint project between the Harvard T.H. Chan School of Public Health and the Human Vaccines Project (HVP), focuses on studying immunity and the predictability of immuneresponsiveness to vaccines in aging populations. This paper describes the hypotheses and methodological approaches of this new collaborative initiative. Central to our thinking is the idea that predictors of age-related non-communicable diseases are the same as predictors for infectious diseases like COVID-19 and influenza. Fundamental to our approach is to differentiate between chronological, biological and immune age, and to use existing large-scale population cohorts. The latter provide well-typed phenotypic data on individuals' health status over time, readouts of routine clinical biochemical biomarkers to determine biological age, and bio-banked plasma samples to deep phenotype humoral immune responses as biomarkers of immune age. The first phase of the program involves 1. the exploration of biological age, humoral biomarkers of immune age, and genetics in a large multigenerational cohort, and 2. the subsequent development of models of immunity in relation to health status in a second, prospective cohort of an aging population. In the second phase, vaccine responses and efficacy of licensed COVID-19 vaccines in the presence and absence of influenza-, pneumococcal- and pertussis vaccines routinely offered to elderly, will be studied in older aged participants of prospective population-based cohorts in different geographical locations who will be selected for representing distinct biological and immune ages. The HII research program is aimed at relating vaccine responsiveness to biological and immune age, and identifying aging-related pathways crucial to enhance vaccine effectiveness in aging populations.

Estimating epidemiologic dynamics from cross-sectional viral load distributions.

Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are confounded by variable testing practices. We show that the population distribution of viral loads observed under random or symptom-based surveillance-in the form of cycle threshold (Ct) values obtained from reverse transcription quantitative polymerase chain reaction testing-changes during an epidemic. Thus, Ct values from even limited numbers of random samples can provide improved estimates of an epidemic's trajectory. Combining data from multiple such samples improves the precision and robustness of this estimation. We apply our methods to Ct values from surveillance conducted during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in a variety of settings and offer alternative approaches for real-time estimates of epidemic trajectories for outbreak management and response.

Estimation of Transmission of COVID-19 in Simulated Nursing Homes With Frequent Testing and Immunity-Based Staffing.

Importance: Nursing homes and other long-term care facilities have been disproportionately impacted by the COVID-19 pandemic. Strategies are urgently needed to reduce transmission in these high-risk populations. Objective: To evaluate COVID-19 transmission in nursing homes associated with contact-targeted interventions and testing. Design, Setting, and Participants: This decision analytical modeling study developed an agent-based susceptible-exposed-infectious (asymptomatic/symptomatic)-recovered model between July and September 2020 to examine SARS-CoV-2 transmission in nursing homes. Residents and staff of a simulated nursing home with 100 residents and 100 staff split among 3 shifts were modeled individually; residents were split into 2 cohorts based on COVID-19 diagnosis. Data were analyzed from September to October 2020. Exposures: In the resident cohorting intervention, residents who had recovered from COVID-19 were moved back from the COVID-19 (ie, infected with SARS-CoV-2) cohort to the non-COVID-19 (ie, susceptible and uninfected with SARS-CoV-2) cohort. In the immunity-based staffing intervention, staff who had recovered from COVID-19 were assumed to have protective immunity and were assigned to work in the non-COVID-19 cohort, while susceptible staff worked in the COVID-19 cohort and were assumed to have high levels of protection from personal protective equipment. These interventions aimed to reduce the fraction of people's contacts that were presumed susceptible (and therefore potentially infected) and replaced them with recovered (immune) contacts. A secondary aim of was to evaluate cumulative incidence of SARS-CoV-2 infections associated with 2 types of screening tests (ie, rapid antigen testing and polymerase chain reaction [PCR] testing) conducted with varying frequency. Main Outcomes and Measures: Estimated cumulative incidence proportion of SARS-CoV-2 infection after 3 months. Results: Among the simulated cohort of 100 residents and 100 staff members, frequency and type of testing were associated with smaller outbreaks than the cohorting and staffing interventions. The testing strategy associated with the greatest estimated reduction in infections was daily antigen testing, which reduced the mean cumulative incidence proportion by 49% in absence of contact-targeted interventions. Under all screening testing strategies, the resident cohorting intervention and the immunity-based staffing intervention were associated with reducing the final estimated size of the outbreak among residents, with the immunity-based staffing intervention reducing it more (eg, by 19% in the absence of testing) than the resident cohorting intervention (eg, by 8% in the absence of testing). The estimated reduction in transmission associated with these interventions among staff varied by testing strategy and community prevalence. Conclusions and Relevance: These findings suggest that increasing the frequency of screening testing of all residents and staff, or even staff alone, in nursing homes may reduce outbreaks in this high-risk setting. Immunity-based staffing may further reduce spread at little or no additional cost and becomes particularly important when daily testing is not feasible.

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes.

Given vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two critical issues arise: How timing of delivery of the second dose will affect infection dynamics and how it will affect prospects for the evolution of viral immune escape via a buildup of partially immune individuals. Both hinge on the robustness of the immune response elicited by a single dose as compared with natural and two-dose immunity. Building on an existing immuno-epidemiological model, we find that in the short term, focusing on one dose generally decreases infections, but that longer-term outcomes depend on this relative immune robustness. We then explore three scenarios of selection and find that a one-dose policy may increase the potential for antigenic evolution under certain conditions of partial population immunity. We highlight the critical need to test viral loads and quantify immune responses after one vaccine dose and to ramp up vaccination efforts globally.