COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition (preprint)

Newborns can acquire immunological protection to SARS-CoV-2 through vaccine-conferred antibodies in human breast milk. However, there are some concerns around lactating mothers with regards to potential short- and long-term adverse events and vaccine-induced changes to their breast milk microbiome composition, which helps shape the early-life microbiome. Here, we recruited 49 lactating mothers from Hong Kong who received two doses of BNT162b2 vaccine between June 2021 and August 2021. Breast milk samples were self-collected by participating mothers pre-vaccination, one week post-first dose, one week post-second dose, and one month post-second dose. The levels of SARS-CoV-2 spike-specific IgA and IgG in breast milk peaked at one week post-second dose. Subsequently, the levels of both antibodies rapidly waned in breast milk, with IgA levels returning to baseline levels one month post-second dose. The richness and composition of human breast milk microbiota changed dynamically throughout the vaccination regimen, but the abundances of beneficial microbes such as Bifidobacterium species did not significantly change after vaccination. In addition, we found that baseline breast milk bacterial composition can predict spike-specific IgA levels at one week post-second dose (Area Under Curve: 0.72, 95% confidence interval: 0.58–0.85). Taken together, our results suggest that infants may acquire immunological protection from breast milk from SARS-CoV-2-vaccinated mothers by both the vertical transmission of antibodies and beneficial microbiota.

Effect of E-beam irradiation on the qualitative attributes of shrimp (Penaeus vannamei)

As a non-thermal food processing technology, Electron beam (E-beam) irradiation has been used to enhance microbial safety by deactivating unwanted spoilage and pathogenic microorganisms in food industry. This study evaluated the effects of E-beam irradiation at doses killing SARS-COV-2 on qualities and sensory attributes. The results showed that irradiation caused little effect on the proximate composition, amino acid content, texture, and sensory attributes (P > 0.05). However, E-beam increased TBARS (Thiobarbituric acid reactive substances) and lowered vitamin E content in dose-dependently. Irradiation up to 10 kGy significantly decreased unsaturated fatty acid (UFA) content and inhibited the increase in TVB-N (The total volatile basic nitrogen) while reducing cohesiveness and chewiness (P < 0.05). E-beam irradiation with 7–10 kGy caused greater ΔE values (ΔE > 5) via the significant increase of b*, accompanied by big visual difference in shrimp (P < 0.05). A dose of 4 kGy E-beam irradiation was recommended without altering its physicochemical properties and sensory attributes.

Unspecific reactivity must be excluded in COVID-19 epidemiological analyses or virus tracing based on serologic testing: Analysis of 46,777 post-pandemic samples and 1,114 pre-pandemic samples

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Serologic testing is complementary to nucleic acid screening to identify SARS-CoV-2. This study aimed to evaluate unspecific reactivity in SARS-CoV-2 serologic tests. Materials and methods Total anti-SARS-CoV-2 antibodies from 46,777 subjects who were screened for SARS-CoV-2 were retrospectively studied to evaluate the incidence and characteristics of the unspecific reactivity. A total of 1,114 pre-pandemic samples were also analysed to compare unspecific reactivity. Results The incidence of unspecific reactivity in anti-SARS-CoV-2 total antibody testing was 0.361% in 46,777 post-pandemic samples, similar to the incidence of 0.359% (4/1,114) in 1,114 pre-pandemic samples (p = 0.990). Subjects ≥ 19 years old had a 2.753-fold [95% confidence interval (CI), 1.130–6.706] higher probability of unspecific reactivity than subjects < 19 years old (p = 0.026). There was no significant difference between the sexes. The unspecific reactivity was associated with 14 categories within the disease spectrum, with three tops being the skin and subcutaneous tissue diseases (0.93%), respiratory system diseases (0.78%) and neoplasms diseases (0.76%). The percentage of patients with a titer ≥ 13.87 cut-off index (COI) in the unspecific reactivity was 7.69%. Conclusion Our results suggest a unspecific reactivity incidence rate of 0.361% involving 14 categories on the disease spectrum. Unspecific reactivity needs to be excluded when performing serologic antibody testing in COVID-19 epidemiological analyses or virus tracing.

Clinical analysis of drug-induced liver dysfunction in COVID-19 patients in the third hospital of Wuhan in 2020

Objective: To investigate the general rules and characteristics of drug-induced liver dysfunction during the treatment of COVID-19, and to provide references for safe clinical use.

Age-related seroprevalence trajectories of seasonal coronaviruses in children (preprint)

Four seasonal coronaviruses, including HCoV-NL63 and HCoV-229E, HCoV-OC43 and HCoV-HKU1 cause approximately 15–30% of common colds in adults. However, the frequency and timing of early infection with four seasonal coronaviruses in the infant are still not well studied. Here, we evaluated the serological response to four seasonal coronaviruses in 1886 children under 18-year-old to construct the viral infection rates. The antibody levels were also determined from the plasma samples of 485 pairs postpartum women and their newborn babies. This passive immunity waned at one year after birth and the resurgence of the IgGs were found thereafter with the increase of the age. Taken together, our results show the age-related seroprevalence trajectories of seasonal coronaviruses in children and provide useful information for deciding vaccine strategy for coronaviruses in the future.

Evolution of disease transmission rate during the course of SARS-COV-2: Patterns and determinants (preprint)

Background: This has been the first time in recent history when extreme measures that have deep and wide impact on our economic and social systems, such as lock downs and border closings, have been adopted at a global scale. These measures have been taken in response to the severe acute respiratory syndrome coronavirus SARS-CoV-2 pandemic, declared a Public Health Emergency of International Concern on 30 January 2020. Epidemic models are being used by governments across the world to inform social distancing and other public health strategies to reduce the spread of the virus. These models, which vary widely in their complexity, simulate interventions by manipulating model parameters that control social mixing, healthcare provision and other behavioral and environmental processes of disease transmission and recovery. The validity of these parameters is challenged by the uncertainty of the impact on disease transmission from socio-economic factors and public health interventions. Although sensitivity of the models to small variations in parameters are often carried out, the forecasting accuracy of these models is rarely investigated during an outbreak. Methods: We fitted a stochastic transmission model on reported cases, recoveries and deaths associated with the infection of SARS-CoV-2 across 101 countries that had adopted at least one social-distancing policy by 15 May 2020. The dynamics of disease transmission was represented in terms of the daily effective reproduction number ( R t ). Countries were grouped according to their initial temporal R t patterns using a hierarchical clustering algorithm. We then computed the time lagged cross correlation among the daily number of policies implemented (policy volume), the daily effective reproduction number, and the daily incidence counts for each country. Finally, we provided forecasts of incidence counts up to 30-days from the time of prediction for each country repeated over 230 daily rolling windows from 15 May to 31 Dec 2020. The forecasting accuracy of the model when R t is updated every time a new prediction is made was compared with the accuracy using a static R t . Findings: We identified 5 groups of countries with distinct transmission patterns during the first 6 months of the pandemic. Early adoption of social distancing measures and a shorter gap between any two interventions were associated with a reduction on the duration of outbreaks (with correlation coefficients of -0.26 and 0.24 respectively). Sustained social distancing appeared to play a role in the prevention of the second transmission peak. By 15 May 2020, the average of the median R t across examined countries had reduced from its peak of 20.5 (17.79, 23.20) to 1.3 (0.94, 1.74).The time lagged cross correlation analysis revealed that increased policy volume was associated with lower future R t (the negative correlation was minimized when R t lagged the policy volume by 75 days), while a lower R t was associated with lower future policy volume (the positive correlation was maximized when R t led by 102 days). R t led the daily incidence counts by 78 days, with lower incidence counts being associated with lower future policy volume (the positive correlation was maximized when counts led the volume by 135 days). On the other hand, higher policy volume was not associated with lower incidence counts within a lag of up to 180 days.The outbreak prediction accuracy of the stochastic transmission model using dynamically updated R t produced an average AUROC of 0.72 (0.708, 0.723) compared to 0.56 (0.555, 0.568) when R t was kept constant. Prediction accuracy declined with forecasting time. Interpretation Understanding the evolution of the daily effective reproduction number during an epidemic is an important complementary piece of information to reported daily counts, recoveries and deaths. This is because R t provides an early signal of the efficacy of containment measures. Using updated R t values produces significantly better predictions of future outbreaks. Our results found a substantial variation in the effect of early public health interventions on the evolution of R t over time and across countries, which could not be explained solely by the timing and number of the adopted interventions. This suggests that further knowledge about the idiosyncrasy of the implementation and effectiveness thereof is required. Although sustained containment measures have successfully lowered growth rate of disease transmission, more than half of the studied countries failed to maintain an effective reproduction number close to or below 1. This resulted in continued growth in reported cases.

Post-Infection Cognitive Impairments in Elderly Patients with COVID-19 (preprint)

Background: Understanding the long-term effects of coronavirus disease 2019 (COVID-19) on cognitive function is essential for the prevention of cognitive decline in elderly population. This study aims to assess cognitive status and longitudinal decline at 6 months post-infection in elderly patients recovered from COVID-19.Methods: This cross-sectional study recruited 1013 COVID-19 inpatients aged over 60 years who were discharged from three COVID-19-designated hospitals in Wuhan, China, from February 10 to March 13, 2020. In total, 262 uninfected living spouses of COVID-19 patients were selected as controls. Subjects were examined for their current cognitive status using a Chinese version of the Telephone Interview of Cognitive Status-40 (TICS-40) and longitudinal cognitive decline using an Informant Questionnaire on Cognitive Decline in the Elderly (IQCODE). Cognitive assessments were performed 6 months after patient discharge.Findings: COVID-19 patients had significantly lower TICS-40 scores (patients: 29.73±6.13; controls: 30.74±5.95, p=0.016) and higher IQCODE scores (patients: 3.40±0.81; controls: 3.15±0.39, p<0.001) than the controls. Severe COVID-19 patients had lower TICS-40 scores and higher IQCODE scores than non-severe COVID-19 patients (TICS-40: 22.98±7.12 vs. 30.46±5.53, p<0.001; IQCODE: 4.06±1.39 vs. 3.33±0.68, p<0.001) and controls (TICS-40: 22.98±7.12 vs. 30.74±5.95, p<0.001; IQCODE: 4.06±1.39 vs. 3.15±0.39, p<0.001). Severe COVID-19 patients had a higher proportion of cases with a current cognitive impairment and longitudinal cognitive decline than non-severe COVID-19 patients and controls. COVID-19 severity (OR: 8.142, 95% CI: 5.007-13.239) was associated with worse current cognitive function. Older age (OR: 1.024, 95% CI: 1.003 to 1.046), COVID-19 severity (OR: 2.277, 95% CI: 1.308 to 3.964), mechanical ventilation (OR: 5.388, 95% CI: 3.007 to 9.656), and hypertension (OR: 1.866, 95% CI: 1.376 to 2.531) were associated with an increased risk of longitudinal cognitive decline.Interpretation: SARS-CoV-2 infection is associated with delayed cognitive decline in elderly population. COVID-19 patients with risk factors, including severe disease, older age, mechanical ventilation, and hypertension, should be intensively monitored for delayed cognitive decline. Funding: National Natural Science Foundation of China.Conflict of Interest: We declared no conflict of interests.Ethical Approval: The study protocols were approved by the institutional review boards of the hospitals. Verbal informed consent was obtained from all participants prior to the survey.

An epidemiological forecast model and software assessing interventions on the COVID-19 epidemic in China

We develop a health informatics toolbox that enables timely analysis and evaluation of the time-course dynamics of a range of infectious disease epidemics. As a case study, we examine the novel coronavirus (COVID-19) epidemic using the publicly available data from the China CDC. This toolbox is built upon a hierarchical epidemiological model in which two observed time series of daily proportions of infected and removed cases are generated from the underlying infection dynamics governed by a Markov Susceptible-Infectious-Removed (SIR) infectious disease process. We extend the SIR model to incorporate various types of time-varying quarantine protocols, including government-level 'macro' isolation policies and community-level 'micro' social distancing (e.g. self-isolation and self-quarantine) measures. We develop a calibration procedure for underreported infected cases. This toolbox provides forecasts, in both online and offline forms, as well as simulating the overall dynamics of the epidemic. An R software package is made available for the public, and examples on the use of this software are illustrated. Some possible extensions of our novel epidemiological models are discussed.

Intravenous Mesenchymal Stem Cells in Extracorporeal Oxygenation Patients with Severe COVID-19 Acute Respiratory Distress Syndrome (preprint)

Background: There is an ongoing critical need to improve therapeutic strategies for COVID-19 pneumonia, particularly in the most severely affected patients. Adult mesenchymal stem cell (MSC) infusions have the potential to benefit critically ill patients with acute respiratory syndrome SARS-COV-2 infection, but clinical data supporting efficacy are lacking. Methods: We conducted a case-control study of critically ill patients with laboratory-confirmed COVID-19, severe acute respiratory distress syndrome (ARDS). To evaluate clinical responsiveness in the most critically ill patient we examined outcomes in a sub-group of those requiring extracorporeal membrane oxygenation (ECMO) support. Patients (n=9) were administered with up to 3 infusions of intravenous (IV) MSCs and compared to a local ECMO control group (n=31). The primary outcome was safety, and the secondary outcomes were all-cause mortality (or rate of hospital discharge), cytokine levels, and viral clearance. Findings: MSC infusions (12 patients) were well tolerated and no side effects occurred. Of ECMO patients receiving MSC infusions, 2 out of 9 died (22.2%; 95%CI: 2.8%, 60.0%) compared with a mortality of 15 of 31 (48.4%; 95%CI: 30.2%, 66.9%; p = 0.25) in the ECMO control group. Isolated plasma exosomes containing the SARS-COV-2 Spike protein decreased after MSC infusions between day 14 or 21 after administration (p=0.003 and p=0.005, respectively) and was associated with a decrease in COVID-19 IgG Spike protein titer at same time points (p = 0.006 and p=0.007, respectively). Control ECMO patients receiving convalescent plasma did not clear COVID-19 IgG over the same time frame. Interpretation: Together these findings suggest that MSC IV infusion is well tolerated in patients with a broad range of severity including the most severe COVID-19 ARDS requiring ECMO. These data also raise the possibility that MSCs, in addition to exerting an immunomodulatory effect, contribute to viral clearance and strongly support the conduct of randomized placebo-controlled trial.

Comparison of acute pneumonia caused by SARS-COV-2 and other respiratory viruses in children: a retrospective multi-center cohort study during COVID-19 outbreak (preprint)

Background: Until July 14, 2020, coronavirus disease-2019 (COVID-19) has infected more than 130 million individuals and has caused a certain degree of panic. Viral pneumonia caused by common viruses such as respiratory syncytial virus, rhinovirus, human metapneumovirus, human bocavirus, and parainfluenza viruses have been more common in children. However, the incidence of COVID-19 in children was significantly lower than that in adults. The purpose of this study was to describe the clinical manifestations, treatment and outcomes of COVID-19 in children compared to those of other sources of viral pneumonia diagnosed during the COVID-19 outbreak. Methods: Children with COVID-19 and viral pneumonia admitted to 20 hospitals were enrolled in this retrospective multi-center cohort study. A total of 64 children with COVID-19 were defined as the COVID-19 cohort, of which 40 children who developed pneumonia were defined as the COVID-19 pneumonia cohort. Another 284 children with pneumonia caused by other viruses were defined as the viral pneumonia cohort. Results: Compared to the viral pneumonia cohort, children in the COVID-19 cohort were mostly exposed to family members confirmed to have COVID-19 (53/64 vs. 23/284), were of older median age (6.3 vs. 3.2 years), and had a higher proportion of ground-glass opacity (GGO) on computed tomography (18/40 vs. 0/38) (all P ＜0.001). Children in the COVID-19 pneumonia cohort had a lower proportion of severe cases (1/40 vs. 38/284, P =0.048), and lower cases with high fever (3/40 vs 167/284, P ＜0.001), requiring intensive care (1/40 vs 32/284, P ＜0.047) and with shorter symptomatic duration (median 5 vs 8 days, P ＜0.001). The proportion of cases with evaluated inflammatory indicators, biochemical indicators related to organ or tissue damage, D-dimer and secondary bacterial infection were lower in the COVID-19 pneumonia cohort than in the viral pneumonia cohort (all P ＜0.05). No statistical differences were found in the duration of positive PCR results from pharyngeal swabs in 25 children with COVID-19 who received antiviral drugs (lopinavir-ritonavir, ribavirin, and arbidol) as compared to duration in 39 children without antiviral therapy [median 10 vs. 9 days, P =0.885]. Conclusion: The symptoms and severity of COVID-19 pneumonia in children were no more severe than those in children with other viral pneumonias. Lopinavir-ritonavir, ribavirin and arbidol do not shorten the duration of positive PCR results from pharyngeal swabs in children with COVID-19. During the COVID-19 outbreak, attention also must be given to children with infection by other pathogens infection.

The immunodominant and neutralization linear epitopes for SARS-CoV-2 (preprint)

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becomes a tremendous threat to global health. Although vaccines against the virus are under development, the antigen epitopes on the virus and their immunogenicity are poorly understood. Here, we simulated the three-dimensional structures of SARS-CoV-2 proteins with high performance computer, predicted the B cell epitopes on spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins of SARS-CoV-2 using structure-based approaches, and then validated the epitope immunogenicity by immunizing mice. Almost all 33 predicted epitopes effectively induced antibody production, six of which were immunodominant epitopes in patients identified via the binding of epitopes with the sera from domestic and imported COVID-19 patients, and 23 were conserved within SARS-CoV-2, SARS-CoV and bat coronavirus RaTG13. We also found that the immunodominant epitopes of domestic SARS-CoV-2 were different from that of the imported, which may be caused by the mutations on S (G614D) and N proteins. Importantly, we validated that eight epitopes on S protein elicited neutralizing antibodies that blocked the cell entry of both D614 and G614 pseudo-virus of SARS-CoV-2, three and nine epitopes induced D614 or G614 neutralizing antibodies, respectively. Our present study shed light on the immunodominance, neutralization, and conserved epitopes on SARS-CoV-2 which are potently used for the diagnosis, virus classification and the vaccine design tackling inefficiency, virus mutation and different species of coronaviruses.

An artificial intelligence system reveals liquiritin inhibits SARS-CoV-2 by mimicking type I interferon (preprint)

The pandemic COVID-19 has spread to all over the world and greatly threatens safety and health of people. COVID-19 is highly infectious and with high mortality rate. As no effective antiviral treatment is currently available, new drugs are urgently needed. We employed transcriptional analysis to uncover potential antiviral drugs from natural products or FDA approved drugs. We found liquiritin significantly inhibit replication of SARS-CoV-2 in Vero E6 cells with EC50 = 2.39 M. Mechanistically, we found liquiritin exerts anti-viral function by mimicking type I interferon. Upregulated genes induced by liquiritin are enriched in GO categories including type I interferon signaling pathway, negative regulation of viral genome replication and etc. In toxicity experiment, no death was observed when treated at dose of 300 mg/kg for a week in ICR mice. All the organ indexes but liver and serum biochemical indexes were normal after treatment. Liquiritin is abundant in licorice tablet (~0.2% by mass), a traditional Chinese medicine. Together, we recommend liquiritin as a competitive candidate for treating COVID-19. We also expect liquiritin to have a broad and potent antiviral function to other viral pathogens, like HBV, HIV and etc.