The Analysis of Oral and Fecal Virome Detects Multiple Novel Emerging Viruses in Snakes

Wild animals are considered reservoirs for emerging and reemerging viruses, such as the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Previous studies have reported that bats and ticks harbored variable important pathogenic viruses, some of which could cause potential diseases in humans and livestock, while viruses carried by reptiles were rarely reported. Our study first conducted snakes' virome analysis to establish effective surveillance of potential transboundary emerging diseases. Consequently, Adenoviridae, Circoviridae, Retroviridae, and Parvoviridae were identified in oral samples from Protobothrops mucrosquamatus, Elaphe dione, and Gloydius angusticeps based on sequence similarity to existing viruses. Picornaviridae and Adenoviridae were also identified in fecal samples of Protobothrops mucrosquamatus. Notably, the iflavirus and foamy virus were first reported in Protobothrops mucrosquamatus, enriching the transboundary viral diversity in snakes. Furthermore, phylogenetic analysis revealed that both the novel-identified viruses showed low genetic similarity with previously reported viruses. This study provided a basis for our understanding of microbiome diversity and the surveillance and prevention of emerging and unknown viruses in snakes.

YOLO-R Based Mask Recognition System with Winograd Convolution Acceleration Chip

In this paper, we proposed 'YOLO-R based mask recognition system with Winograd convolution acceleration chip.' In order to prevent the spread of COVID-19, we proposed a mask recognition system based on YOLO-R that adopted the CSP backbone architecture and used prediction refinement to predict, optimize, and obtain high recognition results. In addition, we designed the Winograd convolution acceleration chip to accelerate the operation of the YOLO-R neural network, so that the system can achieve real-time computing. © 2022 IEEE.

Dynamic changes and clinical significance of COVID-19 specific antibodies in rehabilitated patients

Objective To investigate the dynamic changes and clinical significance of specific antibodies in patients with coronavirus disease 2019 (COVID-19). Methods A retrospective study was conducted to collect 141 adult COVID-19 survivors who were followed up in the Eighth Hospital affiliated to Guangzhou Medical University from February 6, 2020, to March 24, 2021. The patients were divided into severe group (severe and critical) and non-severe group (light and ordinary) according to the diagnosis at discharge. The antibody changes of the two groups were compared and analyzed at 1 week, 2 weeks, 1 month, 3 months, 6 months and 1 year after discharge. Results After discharge from hospital, the positive rate of IgG in the severe group was 95.00% after 1 week and 100.00% in the following year, in the positive rate of IgG in the non-severe group was 59.50% after 1 week, 90.08% in 6 months and 76.03% in one year. The level of serum IgG in the severe group was significantly higher than that in non-severe group (Z=-2.441, P=0.015). One-year follow-up: the serum IgG in the severe group was significantly higher than that in the non-severe group (Z=-3.410, P=0.001). The serum IgM level of the severe group after one year follow-up was lower than that of the six months follow-up, the difference was statistically significant (Z=-2.259, P=0.024). The serum IgG and IgM level of the non-severe group after one year follow-up was lower than that of the six months follow-up, the difference was statistically significant (Z=-7.37, P<0.01;Z=3.850, P<0.01). Conclusion The level of serum protective antibody in COVID-19 patients remained high within 6 months after discharge, and remained stable within 1 year after discharge. The antibody titers in the severe group were significantly higher than those in the non-severe group and lasted for at least one year. COVID-19 survivors receive 1 year of natural immune protection, and patients with critical conditions receive immunity for longer periods of time. © 2022 The authors.

[Clinical characteristics of convalescent children infected with SARS-CoV-2 Omicron variant in Tianjin].

Objective: To analyze the clinical characteristics of SARS-CoV-2 Omicron variant infected children in convalescence in Tianjin. Methods: A total of 104 pediatric patients infected by SARS-CoV-2 Omicron variant Tianjin First Central Hospital (designated hospital for SARS-CoV-2 infection in Tianjin) for convalescent treatment from January 22nd, 2022 to February 24th were included for a retrospective study.Clinical data including clinical typing, SARS-CoV-2 IgG and IgM test and 2019-nCoV nucleic acid test were collected.The cases were divided into 2-dose group and zero-dose group based on the doses of inactivated SARS-CoV-2 vaccine. The children were divided into repositive group and negative group, according to the nucleic acid test during hospitalization. Chi-square test was used for the comparison between the groups. Results: The age of these 104 children was 10.0 (0.3, 14.0) years on admission, 53 children were males and 51 were females, 92 cases (88.5%) had mild symptoms, 12 cases (11.5%) had common symptoms.The age and SARS-CoV-2 IgG level of zero-dose group was lower (2.0 (0.3, 10.2) vs. 10.0 (3.2, 14.0) years, 10 (2, 17) vs. 193 (157, 215), χ²=-5.57, Z=-48.76,both P<0.001) than that of 2-dose group. The zero-dose group had a high rate of transmission among family members and a high level of SARS-CoV-2 IgM level (13/14 vs. 62.2% (56/90), 0.4 (0.2, 0.8) vs. 0.4 (0.2, 1.1),χ²=5.09, Z=-48.95, both P<0.05) than the 2-dose group. Repositive group had a high rate of underlying diseases and SARS-CoV-2 IgM level was higher (2/13) vs. 1.1% (1/91), (0.6 (0.2, 1.0) vs. 0.3 (0.2, 0.7), χ²=8.29, Z=2.70, both P<0.05) than negative group. The SARS-CoV-2 IgG level of repositive group was lower than that of negative group (160 (78, 197) vs. 213 (186, 231), χ²=-3.20, P<0.05). Conclusions: Children infected with SARS-CoV-2 Omicron variant in Tianjin were mainly transmitted by family members, and most of them had mild symptoms. Two-dose group had higher IgG levels and lower IgM levels than zero-dose group.The probability of SARS-CoV-2 nucleic acid test repositivity increased in children with underlying diseases and lower IgG levels.

An improved voterank algorithm to identifying a set of influential spreaders in complex networks

Identifying a set of critical nodes with high propagation in complex networks to achieve maximum influence is an important task in the field of complex network research, especially in the background of the current rapid global spread of COVID-19. In view of this, some scholars believe that nodes with high importance in the network have stronger propagation, and many classical methods are proposed to evaluate node importance. However, this approach makes it difficult to ensure that the selected spreaders are dispersed in the network, which greatly affects the propagation ability. The VoteRank algorithm uses a voting-based method to identify nodes with strong propagation in the network, but there are some deficiencies. Here, we solve this problem by proposing the DILVoteRank algorithm. The VoteRank algorithm cannot properly reflect the importance of nodes in the network topology. Based on this, we redefine the initial voting ability of nodes in the VoteRank algorithm and introduce the degree and importance of the line (DIL) ranking method to calculate the voting score so that the algorithm can better reflect the importance of nodes in the network structure. In addition, the weakening mechanism of the VoteRank algorithm only weakens the information of neighboring nodes of the selected nodes, which does not guarantee that the identified initial spreaders are sufficiently dispersed in the network. On this basis, we consider all the neighbors nodes of the node's nearest and next nearest neighbors, so that the crucial spreaders identified by our algorithm are more widely distributed in the network with the same initial node ratio. In order to test the algorithm performance, we simulate the DILVoteRank algorithm with six other benchmark algorithms in 12 real-world network datasets based on two propagation dynamics model. The experimental results show that our algorithm identifies spreaders that achieve stronger propagation ability and propagation scale and with more stability compared to other benchmark algorithms.

IMPROVED VOTERANK ALGORITHM TO IDENTIFY CRUCIAL SPREADERS IN SOCIAL NETWORKS

In the field of complex networks, Identifying crucial spreaders with high propagation ability is an important aspect of research, especially in the background of the global spread of COVID-19. In view of this, a large number of ranking algorithms and their improved versions have been proposed to evaluate the importance of nodes in the network, such as degree centrality, betweenness centrality, and k-core centrality. However, most of these methods neglect to consider the average shortest path between important nodes in the process of node importance evaluation, which will be difficult to ensure that the initial crucial spreaders have a large influence on the network. Recently, the VoteRank algorithm proposed a new idea for identifying widely distributed key spreaders based on the voting mechanism, but there are some aspects of this algorithm that require improvement. In this paper, we propose a VoteRank improved by degree centrality, k-core, and h-index (DKHVoteRank) for identifying critical spreaders in the complex networks. We introduce additional metrics to optimize the voting mechanism of the VoteRank to ensure that our algorithm can identify a widely distributed spreaders with high importance in the network. We conducted simulation experiments based on the Susceptible-Infected-Recovered (SIR) model on 12 different complex network datasets, and the results show that our proposed algorithm performs significantly better than other benchmark algorithms in terms of propagation capability, propagation scale, and applicability of the algorithm.

Passenger management strategy and evacuation in subway station under Covid-19

Under the background of Covid-19 sweeping the world, safe and reasonable passenger flow management strategy in subway stations is an effective means to prevent the spread of virus. Based on the social force model and the minimum cost model, the movement and path selection behavior of passengers in the subway station are modeled, and a strategy for passenger flow management to maintain a safe social distance is put forward. Take Qingdao Jinggangshan Road subway station of China as the simulation scene, the validity of the simulation model is verified by comparing the measured value and simulation value of the time required for passengers from getting off the train to the ticket gate. Simulation results indicate that controlling the time interval between incoming passengers at the entrance can effectively control the social distance between passengers and reduce the risk of epidemic infection. By comparing the evacuation process of passengers under different initial densities, it is found that the greater the initial density of passengers is, the longer the passengers are at risk social distance. In the process of passenger emergency evacuation, the stairs/escalators and ticket gates are bottleneck areas with high concentration of passenger density, which should be strictly disinfected many times on the basis of strictly checking the health code of incoming passengers and controlling the arrival time interval. The simulation results of this paper verify the harmfulness of passenger emergency evacuation without protective measures, and provide theoretical support for the operation and management of subway station under the epidemic situation.

Design, Preparation and Immune Characterization of SARS-CoV-2 Multi-Epitope Chimeric Protein

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can cause respiratory symptoms such as fever, cough and dyspnea after infection, and Coronavirus Disease 2019 (COVID-19), severe acute respiratory syndrome, and even death can occur in severe cases.SARS-CoV-2 infection has no specific treatment drugs, mainly rely on vaccination to block its transmission.In various structural proteins of SARS-CoV-2, Spike protein (S) and Nucleocapsid protein (N) are the main antigenic proteins, which are also important candidate proteins for developing SARS-CoV-2 vaccine and antibody detection reagents.To express chimeric protein containing multiple epitopes of SARS-CoV-2 by prokaryotic expression system, and to verify the immunogenicity of the chimeric protein, antigenic epitopes of SARS-CoV-2 structural proteins were analyzed and screened by molecular biology software, the selected antigenic epitopes were connected in tandem, and expressed high efficiently in E.coli as a chimeric protein by genetic engineering technology.The soluble chimeric protein of high purity was obtained after purification and renaturation.Mice were immunized with the purified chimeric protein together with MF59 adjuvant, aluminum adjuvant or no adjuvant at different doses respectively.Humoral immunity and cellular immunity induced by the chimeric protein were evaluated by detecting the antibody titer of antiserum and the level of related cytokine.The expressed chimeric protein was in the form of inclusion body and exists in the sediment, soluble chimeric protein was obtained after renaturation.The specific antibodies with high titer were produced in the immunized mice, and strong cellular immunity was induced also.Higher concentration of chimeric protein had better elicited immune effect than the lower concentration of chimeric protein.The immune effect induced by the chimeric protein with MF59 adjuvant was no different from that induced with aluminum adjuvant.This study provides novel ideas for the design and renaturation of SARS-CoV-2 chimeric protein, and the chimeric protein is expected to be used for the development of SARS-CoV-2 recombinant protein vaccine and diagnosis reagent.

The use of online MBSR audio in medical staff during the COVID-19 in China.

OBJECTIVE: This study aims to survey medical staff's acceptance of online Mindfulness-Based Stress Reduction (MBSR) during the Novel Coronavirus Pneumonia (NCP), and to know some information of physical and emotional response of those medical staff who worked at the forefront of COVID-19, through the playback amount of the online MBSR training. MATERIALS AND METHODS: Considering the working environment of medical staff in forefront of NCP, we designed and recorded MBSR audio album including 13 sessions, covering 24 hours of a day, then sent the album to medical staff who had been working in Wuhan, Hubei province, China. We collected the playback amount in each session on February 10th and February 24th, which were one week and three weeks after the album was finished. RESULTS: On February 10th and February 24th, there were separately 5778 and 10640 times of broadcasting. The highest broadcasting frequency session was at 5:00 am, followed by 7:00 am. The least broadcasting frequency sessions were 17:00 pm and 19:00 pm. The broadcasting amount in the 6 periods of the night (from 21:00 pm to 7:00 am) was significantly higher than those in the daytime (from 9:00 am to 19:00 pm), with a statistical difference. The tendency of the amount of playback was consistent, which was not affected by the specific content of the mindfulness exercises. CONCLUSIONS: Online MBSR exercises were well accepted by medical staff in the COVID-19. It may help them relax and reduce the risk of stress reactions. During the NCP, medical staff may have different degrees of sleep and emotional problems, which need to be paid more attention to.

[Detection and evaluation of SARS-CoV-2 nucleic acid contamination in corona virus disease 19 ward surroundings and the surface of medical staff's protective equipment]

OBJECTIVE: To determine the environmental contamination degree of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in corona virus disease 2019 (COVID-19) wards, to offer gui-dance for the infection control and to improve safety practices for medical staff, by sampling and detecting SARS-CoV-2 nucleic acid from the air of hospital wards, the high-frequency contact surfaces in the contaminated area and the surfaces of medical staff's protective equipment in a COVID-19 designated hospital in Wuhan, China. METHODS: From March 11 to March 19, 2020, we collected air samples from the clean area, the buffer room and the contaminated area respectively in the COVID-19 wards using a portable bioaerosol concentrator WA-15. And sterile premoistened swabs were used to sample the high-frequency contacted surfaces in the contaminated area and the surfaces of medical staff's protective equipment including outermost gloves, tracheotomy operator's positive pressure respiratory protective hood and isolation clothing. The SARS-CoV-2 nucleic acid of the samples were detected by real-time fluorescence quantitative PCR. During the isolation medical observation period, those medical staff who worked in the COVID-19 wards were detected for SARS-CoV-2 nucleic acid with oropharyngeal swabs, IgM and IgG antibody in the sera, and chest CT scans to confirm the infection status of COVID-19. RESULTS: No SARS-CoV-2 nucleic acid was detected in the tested samples, including the 90 air samples from the COVID-19 wards including clean area, buffer room and contaminated area, the 38 high-frequency contact surfaces samples of the contaminated area and 16 surface samples of medical staff's protective equipment including outermost gloves and isolation clothing. Moreover, detection of SARS-CoV-2 nucleic acid by oropharyngeal swabs and IgM, IgG antibodies in the sera of all the health-care workers who participated in the treatment for COVID-19 were all negative. Besides, no chest CT scan images of medical staff exhibited COVID-19 lung presentations. CONCLUSION: Good ventilation conditions, strict disinfection of environmental facilities in hospital wards, guidance for correct habits in patients, and strict hand hygiene during medical staff are important to reduce the formation of viral aerosols, cut down the aerosol load, and avoid cross-infection in isolation wards. In the face of infectious diseases that were not fully mastered but ma-naged as class A, it is safe for medical personnel to be equipped at a high level.

[Analysis of bronchoscope-guided tracheal intubation in 12 cases with coronavirus disease 2019 under the personal protective equipment with positive pressure protective hood].

Endotracheal intubation is an independent risk factor for respiratory infectious diseases. We conducted a retrospective study in 12 cases with COVID-19 who underwent endotracheal intubation at ICU of the Guangzhou eighth hospital from January 20 to February 10, 2020. The intubation procedure, anesthetic regimen, and complication were collected and analyzed. The 9 healthcare workers who involved in intubation received virus nucleic acid test and 14 days temperature monitoring. All 12 patients were successfully intubated under the guidance of bronchoscope, without any complications. Midazolam, Propofol and Morphine or fentanyl were used for sedation and analgesia, avoiding patients cough and agitated during the procedure. The 9 healthcare workers were protected under the Personal Protective Equipment(PPE) with positive pressure protective hood. The detection of oropharyngeal swab virus nucleic acid were negative in all 9 healthcare workers, none of them had fever or any respiratory symptoms. The PPE with positive pressure protective hood should be needed to perform bronchoscope-guided endotracheal intubation in patients with COVID-19, it could strengthen to protect healthcare workers from virus exposure.