Serum banks for serological survey of SARS-CoV-2 and emerging infectious diseases (preprint)

In June 2021, Udom et al. published their article in  Transboundary and Emerging Diseases performing a serological survey revealed evidence of anti-N-IgG antibodies suggesting SARS-CoV-2 exposure in both dogs and cats during the first and second coronavirus disease 2019 (COVID-19) outbreaks in Thailand. Seroprevalence studies have proven an important tool to monitor the progression of the COVID-19 pandemic. The duration of immunity of SARS-CoV-2 is crucial for the course of the pandemic and for this reason the monitoring of antibodies against SARS-CoV-2 is important. The serum samples from different periods and regions were valuable in terms of scientific significance for serological survey of SARS-CoV-2 and emerging infectious diseases. In order to preserve the remaining serum samples and ensure the stability of anti-virus antibodies in storage serum samples, we strongly suggest that standard serum banks should be established worldwide.

Modeling of the resilient supply chain system from a perspective of production design changes

Building an effective resilient supply chain system (RSCS) is critical and necessary to reduce the risk of supply chain disruptions in unexpected scenarios such as COVID-19 pandemic and trade wars. To overcome the impact of insufficient raw material supply on the supply chain in mass disruption scenarios, this study proposes a novel RSCS considering product design changes (PDC). An RSCS domain model is first developed from the perspective of PDC based on a general conceptual framework, i.e., function-context-behavior-principle-state-structure (FCBPSS), which can portray complex systems under unpredictable situations. Specifically, the interaction among the structure, state and behavior of the infrastructure system and substance system is captured, and then a quantitative analysis of the change impact process is presented to evaluate the resilience of both the product and supply chain. Next, a case study is conducted to demonstrate the PDC strategy and to validate the feasibility and effectiveness of the RSCS domain model. The results show that the restructured RSCS based on the proposed strategy and model can remedy the huge losses caused by the unavailability of raw materials.

Parents' willingness to vaccinate themselves and their children with the booster vaccine against SARS-CoV-2: A cross-sectional study in Puyang city, China.

We aimed to investigate the hesitancy and willingness of parents to vaccinate themselves and their children with a booster dose against severe acute respiratory syndrome coronavirus 2 and related factors. We conducted a cross-sectional study in Puyang city, China. The information was collected, including demographic characteristics, willingness to receive a booster dose of coronavirus disease 2019 (COVID-19) vaccine, and attitudes and concerns toward COVID-19 and vaccines. Vaccine hesitancy was assessed in individuals completing the first two doses and booster eligible, while vaccine willingness was assessed in those completing the first two doses and not yet booster eligible. Among the participants completing two primary doses while not meeting the booster criteria, 95.4% (1465/1536) and 95.0% (1385/1458) had a willingness to a booster dose of COVID-19 vaccine for themselves and their children, respectively. Among the participants who met the booster criteria, 40.3% had vaccine hesitancy. Vaccine hesitancy and unwillingness tended to occur in people who were younger, less educated, less healthy, and with unsureness of vaccines' efficacy and adverse events (AE). The younger age of children, children in poorer health, and concern about the efficacy and AE of vaccines contributed to the participants' unwillingness to vaccinate their children. We observed a high willingness to the booster dose of COVID-19 vaccine both for the parents and their children, regardless of the eligibility to a booster dose. However, 40% of people had delayed vaccination behaviors. The promotion of scientific knowledge of vaccines' effectiveness and safety is needed, especially for people in poor health and parents with young children. Timely disclosure of AE caused by COVID-19 vaccines and proper aiding offered to people encountering AE are suggested.

Development of a multi-recombinase polymerase amplification assay for rapid identification of COVID-19, influenza A and B.

The coronavirus disease 2019 (COVID-19) pandemic caused extensive loss of life worldwide. Further, the COVID-19 and influenza mix-infection had caused great distress to the diagnosis of the disease. To control illness progression and limit viral spread within the population, a real-time reverse-transcription PCR (RT-PCR) assay for early diagnosis of COVID-19 was developed, but detection was time-consuming (4-6 h). To improve the diagnosis of COVID-19 and influenza, we herein developed a recombinase polymerase amplification (RPA) method for simple and rapid amplification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 and Influenza A (H1N1, H3N2) and B (influenza B). Genes encoding the matrix protein (M) for H1N1, and the hemagglutinin (HA) for H3N2, and the polymerase A (PA) for Influenza B, and the nucleocapsid protein (N), the RNA-dependent-RNA polymerase (RdRP) in the open reading frame 1ab (ORF1ab) region, and the envelope protein (E) for SARS-CoV-2 were selected, and specific primers were designed. We validated our method using SARS-CoV-2, H1N1, H3N2 and influenza B plasmid standards and RNA samples extracted from COVID-19 and Influenza A/B (RT-PCR-verified) positive patients. The method could detect SARS-CoV-2 plasmid standard DNA quantitatively between 102 and 105 copies/ml with a log linearity of 0.99 in 22 min. And this method also be very effective in simultaneous detection of H1N1, H3N2 and influenza B. Clinical validation of 100 cases revealed a sensitivity of 100% for differentiating COVID-19 patients from healthy controls when the specificity was set at 90%. These results demonstrate that this nucleic acid testing method is advantageous compared with traditional PCR and other isothermal nucleic acid amplification methods in terms of time and portability. This method could potentially be used for detection of SARS-CoV-2, H1N1, H3N2 and influenza B, and adapted for point-of-care (POC) detection of a broad range of infectious pathogens in resource-limited settings.

Inducing supplier backup via manufacturer information sharing under supply disruption risk.

What comes along with the repeating and wide-range COVID-19 outbreak is the increasingly latent supply disruption risk encountered by global supply chains. Among many instruments to enhance supply chain resilience, backup production may be an appropriate choice, whereas how to induce the supplier backup becomes an obstacle. In this study, we investigate a supply chain in the context of the crisis-like new normal with supply disruption risk, wherein a manufacturer uses private demand information as a strategic lever, according to which a supplier decides whether to adopt backup production. Our findings reveal that the supplier's equilibrium decision on the adoption of backup production exhibits a cutoff structure when the manufacturer shares demand information. Moreover, we uncover the effect of information sharing on backup decision. In specific, information sharing impedes the adoption of backup production under low demand potential while promoting it under high demand potential. Interestingly, the manufacturer may have the incentive to share the demand information with the upstream supplier if the demand variability is low and the backup cost is moderate, and such information sharing stimulates the supplier to adopt the backup production. Counterintuitively, the manufacturer and the whole supply chain may display nonmonotonic relations to the backup cost as a result.

Elective surgery scheduling under uncertainty in demand for intensive care unit and inpatient beds during epidemic outbreaks.

Amid the epidemic outbreaks such as COVID-19, a large number of patients occupy inpatient and intensive care unit (ICU) beds, thereby making the availability of beds uncertain and scarce. Thus, elective surgery scheduling not only needs to deal with the uncertainty of the surgery duration and length of stay in the ward, but also the uncertainty in demand for ICU and inpatient beds. We model this surgery scheduling problem with uncertainty and propose an effective algorithm that minimizes the operating room overtime cost, bed shortage cost, and patient waiting cost. Our model is developed using fuzzy sets whereas the proposed algorithm is based on the differential evolution algorithm and heuristic rules. We set up experiments based on data and expert experience respectively. A comparison between the fuzzy model and the crisp (non-fuzzy) model proves the usefulness of the fuzzy model when the data is not sufficient or available. We further compare the proposed model and algorithm with several extant models and algorithms, and demonstrate the computational efficacy, robustness, and adaptability of the proposed framework.

Clinical predictors and RT-PCR profile of prolonged viral shedding in patients with SARS-CoV-2 Omicron variant in Shanghai: A retrospective observational study

Objective To evaluate determinants of prolonged viral RNA shedding in hospitalized patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant infection. Materials and methods Hospitalized patients tested SARS-CoV-2 positive by nasopharyngeal real-time reverse transcriptase-polymerase chain reaction (RT-PCR) were included in the single-center, retrospective study. Patients were divided into 2 groups according to the timing of viral clearance (≤ 8 days, “early clearance” and ≥15 days, “late clearance”). Results 4,084 patients were included in the study (1,023 late clearance, 3,061 early clearance), with median age of 50 years and a higher proportion (61.4%) of male. Univariate analyses showed that comorbidities (including hypertension, diabetes, and coronary heart disease), receiving vaccine, the number of vaccinations, cycle threshold (Ct) open reading frame 1ab (ORF 1ab), and nucleocapsid protein (N) gene values on admission were associated with late viral clearance. In the multivariable analysis, the number of vaccinations (P = 0.010) and Ct ORF 1ab gene (P < 0.001) values on admission were significantly associated with late viral clearance. Generalized Estimating Equations (GEE) analysis showed that the Ct value of ORF 1ab gene and N gene remained unchanged within 3 days, and showed progressively higher values with increasing days during late viral RNA clearance. Conclusion The number of vaccinations and Ct values of ORF 1ab gene were independently associated with a prolonged SARS-CoV-2 RNA shedding.

A "Plug-and-Display" Nanoparticle Vaccine Platform Based on Outer Membrane Vesicles Displaying SARS-CoV-2 Receptor-binding Domain.

Biomimetic nanoparticles obtained from bacteria or viruses have attracted substantial interest in vaccine research and development. Outer membrane vesicles (OMVs) are mainly secreted by gram-negative bacteria during average growth, with a nano-sized diameter and self-adjuvant activity, which may be ideal for vaccine delivery. OMVs have functioned as a multifaceted delivery system for proteins, nucleic acids, and small molecules. To take full advantage of the biological characteristics of OMVs, bioengineered Escherichia coli-derived OMVs were utilized as a carrier and SARS-CoV-2 receptor-binding domain (RBD) as an antigen to construct a "Plug-and-Display" vaccine platform. The SpyCatcher (SC) and SpyTag (ST) domains in Streptococcus pyogenes were applied to conjugate OMVs and RBD. The Cytolysin A (ClyA) gene was translated with the SC gene as a fusion protein after plasmid transfection, leaving a reactive site on the surface of the OMVs. After mixing RBD-ST in a conventional buffer system overnight, covalent binding was formed between the OMVs and RBD. Thus, a multivalent-displaying OMV vaccine was achieved. By replacing with diverse antigens, the OMVs vaccine platform can efficiently display a variety of heterogeneous antigens, thereby potentially rapidly preventing infectious disease epidemics. This protocol describes a precise method for constructing the OMV vaccine platform, including production, purification, bioconjugation, and characterization.

A highly powerful nonspecific strategy to reduce COVID-19 deaths.

The coronavirus disease 2019 (COVID-19) pandemic caused by the coronavirus severe acute respiratory syndrome coronavirus 2 remains risky worldwide. We elucidate here that good IDM (isolation, disinfection, and maintenance of health) is powerful to reduce COVID-19 deaths based on the striking differences in COVID-19 case fatality rates among various scenarios. IDM means keeping COVID-19 cases away from each other and from other people, disinfecting their living environments, and maintaining their health through good nutrition, rest, and treatment of symptoms and pre-existing diseases (not through specific antiviral therapy). Good IDM could reduce COVID-19 deaths by more than 85% in 2020 and more than 99% in 2022. This is consistent with the fact that good IDM can minimize co-infections and maintain body functions and the fact that COVID-19 has become less pathogenic (this fact was supported with three novel data in this report). Although IDM has been frequently implemented worldwide to some degree, IDM has not been highlighted sufficiently. Good IDM is relative, nonspecific, flexible, and feasible in many countries, and can reduce deaths of some other relatively mild infectious diseases. IDM, vaccines, and antivirals aid each other to reduce COVID-19 deaths. The IDM concept and strategy can aid people to improve their health behavior and fight against COVID-19 and future pandemics worldwide.

The Impact of Active Screening and Management on COVID-19 in Plateau Region of Sichuan, China.

Background: In December 2019, the cases of pneumonia of unknown etiology emerged in Wuhan, China, and rapidly spread throughout the country. The disease was later designated by the World Health Organization (WHO) as Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Few studies have assessed the clinical characteristics of COVID-19 and control strategies used to mitigate disease spread in high-altitude plateau regions of China. Study Objective: To assess the impact of real-world strategies to control COVID-19 spread in remote plateau regions. Methods: A retrospective study was performed to assess the epidemiology of COVID-19 and strategies used to control disease spread in the high-altitude plateau of Sichuan, China from 24 January 2020 to 19 March 2020. Results: COVID-19 spread and outbreaks in Sichuan were attributed to mass gatherings. A total of 70 patients and 20 asymptomatic individuals were found in the hypoxic plateau region of Sichuan. Twelve patients were admitted after the onset of symptoms, while 58 patients and 20 asymptomatic individuals were found by active screening. The symptomatic patients included those with uncomplicated illness (16/70, 22.9%), mild pneumonia (44/70, 62.9%), and severe pneumonia (10/70, 14.3%). Most patients in the study area showed relatively mild and atypical symptoms such as low or no fever and dyspnea. The incidence of severe pneumonia, fever, dyspnea, and interstitial abnormalities identified by chest CT were all significantly lower in screened patients than those admitted after symptom onset (P < 0.05). Severe pneumonia was noted in patients with chronic conditions like hypertension, diabetes etc. as compared to less severe pneumonia in healthy subjects (P <0.05). No patients died and all were eventually discharged. Conclusion: Mass gatherings increased risk of spread of SARS-CoV-2 responsible for COVID-19. Active screening and early management have collectively contributed to reduced incidence of severe pneumonia and satisfactory prognoses of infections with COVID-19 in this hypoxic plateau region.

Driving is believing: Using telepresence robots to access makerspace for teachers in rural areas

This study explored two different ways for K‐12 school teachers to access educational makerspace through virtual fieldtrips. K‐12 school teachers from rural areas of the Southeast USA were divided into two groups. The experimental group (n = 48) drove telepresence robots to take their fieldtrip, while the comparison group (n = 23) watched the same fieldtrip through a recorded video. Analyses of the quantitative and qualitative data, collected through surveys and written reflections, showed that the experimental group reported significantly higher scores in embodiment, social presence and engagement (ie, behaviour, emotion and cognition) than the comparison group, and that actual driving the robots for the virtual fieldtrips was highlighted as a favored experience. Educational significance and implications are discussed. Practitioner notes What is currently known about this topic With makerspaces gaining increasing attention in K‐12 education, professional development (PD) opportunities are needed to help teachers understand makerspaces and related technologies. Teachers in rural areas are faced with the challenges of accessing makerspace resources and opportunities, especially during the COVID‐19 pandemic. Little research has explored teacher makerspace PD in rural areas. Maker resource deficiency in rural areas and the COVID‐19 pandemic call for an alternative approach to the makerspace PD, particularly for teachers in rural areas. What this paper adds Explored the use of telepresence robots for rural teachers to access an authentic makerspace through virtual fieldtrips. Examined the effects of virtual fieldtrip to access makerspaces on K‐12 teachers' embodiment, social presence and engagement. Examined the aspects of the telepresence fieldtrip that were most valuable to K‐12 teachers. Investigated the factors that contribute to teachers' engagement in a virtual fieldtrip. Implications for practitioners Telepresence robot was an effective tool that enabled teachers in rural areas to explore authentic makerspaces through a virtual trip over distance. To help teachers conceptualize the idea of makerspace, it is important to allow teachers to move in the physical makerspace and interact with the environment. To design an engaging fieldtrip that triggers active learning, more attention should be given to how to develop the emotional aspect of a fieldtrip experience. Embodiment plays an important role in virtual fieldtrips. When teachers have a higher level of embodiment, they are more likely to be emotionally and cognitively engaged in a fieldtrip experience. What is currently known about this topic With makerspaces gaining increasing attention in K‐12 education, professional development (PD) opportunities are needed to help teachers understand makerspaces and related technologies. Teachers in rural areas are faced with the challenges of accessing makerspace resources and opportunities, especially during the COVID‐19 pandemic. Little research has explored teacher makerspace PD in rural areas. Maker resource deficiency in rural areas and the COVID‐19 pandemic call for an alternative approach to the makerspace PD, particularly for teachers in rural areas. What this paper adds Explored the use of telepresence robots for rural teachers to access an authentic makerspace through virtual fieldtrips. Examined the effects of virtual fieldtrip to access makerspaces on K‐12 teachers' embodiment, social presence and engagement. Examined the aspects of the telepresence fieldtrip that were most valuable to K‐12 teachers. Investigated the factors that contribute to teachers' engagement in a virtual fieldtrip. Implications for practitioners Telepresence robot was an effective tool that enabled teachers in rural areas to explore authentic makerspaces through a virtual trip over distance. To help teachers conceptualize the idea of makerspace, it is important to allow teachers to move in the physical makerspace and interact with the environment. To design an engagi g fieldtrip that triggers active learning, more attention should be given to how to develop the emotional aspect of a fieldtrip experience. Embodiment plays an important role in virtual fieldtrips. When teachers have a higher level of embodiment, they are more likely to be emotionally and cognitively engaged in a fieldtrip experience. [ FROM AUTHOR] Copyright of British Journal of Educational Technology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Novel Synthetic Lipopeptides as Potential Mucosal Adjuvants Enhanced SARS-CoV-2 rRBD-Induced Immune Response.

As TLR2 agonists, several lipopeptides had been proved to be candidate vaccine adjuvants. In our previous study, lipopeptides mimicking N-terminal structures of the bacterial lipoproteins were also able to promote antigen-specific immune response. However, the structure-activity relationship of lipopeptides as TLR2 agonists is still unclear. Here, 23 synthetic lipopeptides with the same lipid moiety but different peptide sequences were synthesized, and their TLR2 activities in vitro and mucosal adjuvant effects to OVA were evaluated. LP1-14, LP1-30, LP1-34 and LP2-2 exhibited significantly lower cytotoxicity and stronger TLR2 activity compared with Pam2CSK4, the latter being one of the most potent TLR2 agonists. LP1-34 and LP2-2 assisted OVA to induce more profound specific IgG in sera or sIgA in BALF than Pam2CSK4. Furthermore, the possibility of LP1-34, LP2-2 and Pam2CSK4 as the mucosal adjuvant for the SARS-CoV-2 recombinant RBD (rRBD) was investigated. Intranasally immunized with rRBD plus either the novel lipopeptide or Pam2CSK4 significantly increased the levels of specific serum and respiratory mucosal IgG and IgA, while rRBD alone failed to induce specific immune response due to its low immunogenicity. The novel lipopeptides, especially LP2-2, significantly increased levels of rRBD-induced SARS-CoV-2 neutralizing antibody in sera, BALF and nasal wash. Finally, Support vector machine (SVM) results suggested that charged residues in lipopeptides might be beneficial to the agonist activity, while lipophilic residues might adversely affect the agonistic activity. Figuring out the relationship between peptide sequence in the lipopeptide and its TLR2 activity may lay the foundation for the rational design of novel lipopeptide adjuvant for COVID-19 vaccine.

SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells.

Single-cell RNA-seq (scRNA-seq) profiles gene expression with high resolution. Here, we develop a stepwise computational method-called SCAPTURE to identify, evaluate, and quantify cleavage and polyadenylation sites (PASs) from 3' tag-based scRNA-seq. SCAPTURE detects PASs de novo in single cells with high sensitivity and accuracy, enabling detection of previously unannotated PASs. Quantified alternative PAS transcripts refine cell identity analysis beyond gene expression, enriching information extracted from scRNA-seq data. Using SCAPTURE, we show changes of PAS usage in PBMCs from infected versus healthy individuals at single-cell resolution.

Preparation of different fragments of SARS-co V-2 urine protein and its application in fluorescent layer system

Expression and purification of different fragments of the new coronavirus nucleocapsid (N) protein, establish a new coronavirus total antibody fluorescence immunochromatographic method and evaluate the influence of different protein fragments on the method. Using bioinformatics technology to analyze, synthesize, express and purify the N protein sequence, prepare different N protein fragments;use 1-ethyl-(3-dimethylaminopropyl) carbodiimide (1-( 3-Dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) method of fluorescent microspheres coupled with antigen was established to establish a sandwich fluorescence chromatography antibody detection method, and the performance was evaluated respectively. In the prepared 4 N protein fragments, the full-length N protein (N419) is preferably coated, and N412 is labeled with 0.5mol/L NaCl as the optimal combination;the 91-120th amino acid (N412) of the N-terminus of the N antigen is deleted It can reduce 87.5% of non-specific interference;the linear range is 0.312-80U/L, the lowest detection limit is 0.165U/L, and the accuracy is above 95%. The fluorescence immunochromatographic detection method for total antibodies of the new coronavirus established by pairing the N protein fragments has a total coincidence rate of 98% compared with the Guangzhou Wanfu test strip. The improvement provides experimental basis and reference.

[Preparation of different fragments of SARS-CoV-2 N protein and its application in fluorescence chromatography].

Different fragments of SARS-CoV-2 nucleocapsid (N) protein were expressed and purified, and a fluorescence immunochromatography method for detection of SARS-CoV-2 total antibody was established. The effect of different protein fragments on the performance of the method was evaluated. The N protein sequence was analyzed by bioinformatics technology, expressed in prokaryotic cell and purified by metal ion affinity chromatography column. Different N protein fragments were prepared for comparison. EDC reaction was used to label fluorescence microsphere on the synthesized antigen to construct sandwich fluorescence chromatography antibody detection assay, and the performance was systemically evaluated. Among the 4 prepared N protein fragments, the full-length N protein (N419) was selected as the optimized coating antigen, N412 with 0.5 mol/L NaCl was used as the optimal combination; deleting 91-120 amino acids from the N-terminal of N412 reduced non-specific signal by 87.5%. the linear range of detection was 0.312-80 U/L, the limit of detection was 0.165 U/L, and the accuracy was more than 95%. A fluorescence immunochromatographic detection method for analysis of SARS-CoV-2 total antibody was established by pairing N protein fragments. The detection result achieved 98% concordance with the commercially available Guangzhou Wanfu test strip, which is expected to be used as a supplementary approach for detection of SARS-CoV-2. The assay could also provide experimental reference for improving the performance of COVID-19 antibody detection reagents.