Effect of HSP90AB1 on the replication of avian infectious bronchitis virus

The effects of heat shock protein HSPQOABl on the replication of avian infectious bronchitis virus(AIBV) were confirmed by using over expression and RNA interference methods. The results showed that over expression of HSPQOABI inhibited AIBV replication, whereas knockdown of HSPQOABl in- creased AIBV replication. These results indicated that HSPQOABI is a potential anti-viral host factor. These findings provide the basis for further study of the pathogenic mechanism of AIBV and anti-coronavirus infection.

Detection of co-infection of porcine circovirus and porcine epidemic diarrhea virus

In this study, 650 tissue samples which were collected from 16 pig farms in Hubei Province, were used to detect porcine circovirus (PCV) and Porcine epidemic diarrhea virus (PEDV). The results showed that the positive rates of PCV1, PCV2, PCV3 and PEDV single infection were 1.08%, 4.15%, 2.46% and 6.46%, respectively. In the double infections, PEDV+PCV2 had the highest positive rate of 3.54%, followed by PCV2+PCV3, with a positive rate of 1.54%. In multiple infections, PEDV+PCV2+PCV3 had the highest positive rate of 2.00%. The results indicated that the positive rates of PEDV and PCV were decreased compared with the previous studies, but the prevalence of PEDV and PCV was still wide in Hubei Province, and most of which were co-infection.

PVT-COV19D: Pyramid Vision Transformer for COVID-19 Diagnosis (preprint)

With the outbreak of COVID-19, a large number of relevant studies have emerged in recent years. We propose an automatic COVID-19 diagnosis framework based on lung CT scan images, the PVT-COV19D. In order to accommodate the different dimensions of the image input, we first classified the images using Transformer models, then sampled the images in the dataset according to normal distribution, and fed the sampling results into the modified PVTv2 model for training. A large number of experiments on the COV19-CT-DB dataset demonstrate the effectiveness of the proposed method.

Birds carry a diversity of significant viruses in their virome (preprint)

Birds can carry and transmit viruses to humans and other animals. Thus, understanding the viral community hosted by birds could help us predict future outbreaks of human disease. A recent metagenomics study took a broad look at the viruses found in the gut of wild and captive birds. The dataset included samples from over 3,000 birds that represented over 87 species and 10 different phylogenetic orders and the researchers characterized genomes from numerous viral families including astroviruses, coronaviruses, parvoviruses, and adenoviruses. Examining trends, they found that wild birds had higher viral diversity than captive birds. There was also evidence of potential cross-species transmission between wild birds and domestic poultry. Further analysis of the viral genomic sequences revealed differences in virus distribution patterns between wild and captive birds. Different phylogenetic orders of birds and geographic sites also had distinct distribution patterns. Interestingly, there were no significant differences in virus distribution patterns between migratory and resident birds. While further studies are needed to explore the diversity and potential pathogenicity of these viruses in more detail, this study expanded our understanding of viral diversity in birds.

The Therapeutic Target and Mechanism of Vitamin A in Patients with Hepatocholangiocarcinoma and SARS-CoV-2 (preprint)

Objectives: Recent reports indicate patients with hepatocholangiocarcinoma (CHOL) may increase the risk of morbidity and death-rate for coronavirus disease-2019 (SARS-CoV-2). Clinically, anti-CHOL/SARS-CoV-2 medicine is marked scarcity. Vitamin A (VA) refers to a potent nutrient that can achieve anti-cytotoxic and anti-inflammatory actions. Therefore, this study aimed to determine the potential functions and molecular mechanism of VA-exerted effects for clinical treatment of CHOL/SARS-CoV-2.Methods: In methodology, the transcriptome profiling of hepatocholangiocarcinoma patients in the Cancer Genome Analysis (TCGA) was used. Furthermore, the network pharmacology approach and bioinformatics assay were applied for identifying and revealing the molecular functions, therapeutic biotargets, and signaling of niacin against CHOL/SARS-CoV-2.Results: Firstly, the clinical findings identified medical characterizations of CHOL patients with SARS-CoV-2, such as susceptibility gene, prognosis, recurrence, and survival rate. Additionally, the current data uncovered the candidate/vital biotargets, pharmacological functions/pathways of VA against CHOL/SARS-CoV-2. These bioinformatics findings illustrated that VC may contribute to clinical therapy of CHOL/SARS-CoV-2 achieved by induction of cell repair, suppression of oxidative stress and inflammatory reaction, and amelioration of immunity. Attractively, 9 vital therapeutic targets of niacin against CHOL/SARS-CoV-2 were screened and identified, detailed as BRD2, NOS2, GPT, MAPK1, CXCR3, ICAM1, CDK4, CAT, TMPRSS13.Conclusions: In current study, for the first time, the bioinformatics findings uncovered the VA-achieved pharmacological biotarget, function and mechanism for potentially treating CHOL/SARS-CoV-2, as SARS-CoV-2 is still a life-threatening pandemic worldwide.Funding Statement: This study is supported by the National Natural Science Foundation of China (No. 81560134, 81660091) and the National Natural Science Foundation of Guangxi (No.2019GXNSFBA185015, 2018GXNSFAA281242). Declaration of Interests: All the authors have disclosed that they do not have any conflicts of interest.

Incidence rate, clinical course and risk factor for recurrent PCR positivity in discharged COVID-19 patients in Guangzhou, China: a prospective cohort study (preprint)

Background: The phenomenon of COVID-19 patients tested positive for SARS-CoV-2 after discharge (redetectable as positive, RP) emerged globally. The data of incidence rate and risk factors for RP event and the clinical features of RP patients may provide recommendations for virus containment and discharge assessment for COVID-19. Methods: The baseline included 285 adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Guangzhou Eighth People's Hospital. We started the Observation on Jan 20, 2020, and acquired all their definite clinical outcome (becoming RP or keeping normal during post-discharge surveillance) by Mar 10, 2020. The dynamic clinical data of patients during observation were prospectively collected and analyzed. Univariate and multivariate-adjusted logistic regression were used to explore the risk factors related to RP events in COVID-19 patients. Results: By March 10, 27 (9.5%) discharged patients had tested positive for SARS-CoV-2 in their nasopharyngeal swab after a median duration of 7·0 days (IQR 5·0-8·0). Age, sex, epidemiological history, clinical symptoms and underlying diseases were similar between RP and non-RP patients (p>0.05). Compared to first admission, RP patients generally had milder clinical symptoms, lower viral load, shorter length of stay and improved pulmonary conditions at readmission (p<0.05). Elder RP patients (≥ 60 years old) were more likely to be symptomatic compared to younger patients (7/8, 87.5% vs. 3/19, 18.8%, p=0.001) at readmission. A prolonged duration of viral shedding (>10 days) during the first hospitalization [adjusted odds ratio [aOR]: 5.82, 95% confidence interval [CI]: 2.50-13.57 for N gene; aOR: 9.64, 95% CI: 3.91-23.73 for ORF gene] and higher Ct value (ORF) in the third week of the first hospitalization (aOR: 0.69; 95% CI: 0.50-0.95) were associated with RP events. Conclusions: RP events occurred in nearly 10% of COVID-19 patients which deserves globally attention. During hospitalization, patients’ low efficiency of viral clearance was a risk factor for RP event. Elderly RP patients were more likely to develop clinical symptoms. To reduce the possibility of reinfection and readmission during the management of COVID-19, more rigorously monitoring on patients’ viral load should be carried out especially in elder patients and later stage of hospitalization.

Effect of large-scale testing platform in prevention and control of the COVID-19 pandemic: an empirical study with a novel numerical model (preprint)

Background: China adopted an unprecedented province-scale quarantine since January 23rd 2020, after the novel coronavirus (COVID-19) broke out in Wuhan in December 2019. Responding to the challenge of limited testing capacity, large-scale standardized and fully-automated laboratory (Huo-Yan) was built as an ad-hoc measure. There was so far no empirical data or mathematical model to reveal the impact of the testing capacity improvement since the quarantine. Methods: We integrated public data released by the Health Commission of Hubei Province and Huo-Yan Laboratory testing data into a novel differential model with non-linear transfer coefficients and competitive compartments, to evaluate the trends of suspected cases under different nucleic acid testing capacities. Results: Without the establishment of Huo-Yan, the suspected cases would increased by 47% to 33,700, the corresponding cost of the quarantine would be doubled, and the turning point of the increment of suspected cases and the achievement of "daily settlement" (all daily new discovered suspected cases were diagnosed according to the nucleic acid testing results) would be delayed for a whole week and 11 days. If the Huo-Yan Laboratory could ran at its full capacity, the number of suspected cases could started to decrease at least a week earlier, the peak of suspected cases would be reduced by at least 44% and the quarantine cost could be reduced by more than 72%. Ideally, if a daily testing capacity of 10,500 could achieved immediately after the Hubei lockdown, "daily settlement" for all suspected cases would be achieved immediately. Conclusions: Large-scale and standardized clinical testing platform with nucleic acid testing, high-throughput sequencing and immunoprotein assessment capabilities need to be implemented simultaneously in order to maximize the effect of quarantine and minimize the duration and cost. Such infrastructure like Huo-Yan, is of great significance for the early prevention and control of infectious diseases for both common times and emergencies.

Experience of treating severe cases of 2019 novel coronavirus pneumonia in Changde area / 中华危重病急救医学

Since the cluster of the 2019 novel coronavirus (2019-nCoV) pneumonia, a large number of patients gathered, the mortality of critical patients has remained high and the treatment was unclear. In this outbreak, Hunan Changde region immediately set up a hospital and intensive care unit. The patients relieved through respiratory support, hemodynamics management, nutritional support, the application of antiviral drugs, analgesic and sedation. The treatment experience in severe cases of 2019-nCov pneumonia patients were summarized as follows: in terms of respiratory support, we needed to pay attention to the advantages of high-flow nasal cannula oxygen therapy (HFNC) and the intervention of mechanical ventilation, pay attention to the ventilator parameters, and adopt prone position timely. In the aspects of fluid resuscitation and volume management, we should pay attention to the characteristics of severe patients' volume status, perform early evaluation, and clinicians should focused on hemodynamic management beside the bed. In the aspect of nutritional support and evaluation and maintenance of intestinal function, early enteral nutrition should be adopted in time. However, the trade-off between the risk of intestinal function and nutritional support in patients with mechanical ventilation and the antiviral benefits of Kaletra needed to be reevaluated, the optimized way of analgesia and sedation was adopted, at the same time, the usage and side effects of antiviral drugs should be paid attention to. We should grasp the opportunity of transportation for severe patients. It is suggested that some warning scores should be used to facilitate early recognition of patients with severe infection and then they should be earlier transferred to the designated hospital for intensive care.