Chicken intestinal microbiota modulation of resistance to nephropathogenic infectious bronchitis virus infection through IFN-I.

BACKGROUND: Mammalian intestinal microbiomes are necessary for antagonizing systemic viral infections. However, very few studies have identified whether poultry commensal bacteria play a crucial role in protecting against systemic viral infections. Nephropathogenic infectious bronchitis virus (IBV) is a pathogenic coronavirus that causes high morbidity and multiorgan infection tropism in chickens. RESULTS: In this study, we used broad-spectrum oral antibiotics (ABX) to treat specific pathogen free (SPF) chickens to deplete the microbiota before infection with nephropathogenic IBV to analyze the impact of microbiota on IBV infections in vivo. Depletion of the SPF chicken microbiota increases pathogenicity and viral burden following IBV infection. The gnotobiotic chicken infection model further demonstrated that intestinal microbes are resistant to nephropathogenic IBV infection. In addition, ABX-treated chickens showed a severe reduction in macrophage activation, impaired type I IFN production, and IFN-stimulated gene expression in peripheral blood mononuclear cells and the spleen. Lactobacillus isolated from SPF chickens could restore microbiota-depleted chicken macrophage activation and the IFNAR-dependent type I IFN response to limit IBV infection. Furthermore, exopolysaccharide metabolites of Lactobacillus spp. could induce IFN-ß. CONCLUSIONS: This study revealed the resistance mechanism of SPF chicken intestinal microbiota to nephropathogenic IBV infection, providing new ideas for preventing and controlling nephropathogenic IBV. Video abstract.

Risk factors of severe and critical patients with COVID-19 in Hubei, China. (Special Issue: Spatio-temporal dynamics analysis, risk assessment and emergency management for COVID-19 epidemic.) [Chinese]

Objective: To investigate the risk factors of severe and critical patients with coronavirus disease 2019(COVID-19)in Hubei, China. Methods All patients with COVID-19 registered in the National Legal Infectious Disease Reporting System of Hubei Provincial Center for Disease Control and Prevention, as of March 18, 2020, were recruited. According to the symptoms, the patients were divided into two groups: mild/moderate patients and severe/critical patients. Their general characteristics were described, and the risk factors of severe and critical patients with COVID-19 were explored by using a Logistic regression model. Results A total of 48 814 cases were included, of which 38 730 were mild/moderate patients and 10 084 were severe/critical patients. The median age was 54(41, 65)years. Multivariate analysis showed that the elderly, male, home workers, people in Wuhan City, migrants, longer interval between onset and diagnosis, low temperature, higher concentrations of PM2.5/PM10/SO2/O3 increased the risk of severe/critical diagnosis in patients with COVID-19. Conclusion The elderly, male, home workers, people in Wuhan City, migrants, longer interval between onset and diagnosis, low temperature, and air pollution exposure are risk factors for severe/critical COVID-19 patients. More attention should be paid to people with these characteristics.

Efficacy and safety of short-wave diathermy treatment for moderate COVID-19 patients: a prospective, double-blind, randomized controlled clinical study.

BACKGROUND: Millions of human beings have suffered in the epidemic of Coronavirus disease 2019 (COVID-19), but until now the effective treatment methods have been limited. AIM: This study aimed to evaluate the efficacy and safety of short-wave diathermy (SWD) treatment for moderate COVID-19 patients. DESIGN: A prospective, double-blind, randomized controlled clinical study. SETTING: Inpatients Unit of a COVID-19 specialized hospital. POPULATION: Forty-two patients with moderate COVID-19 were randomly allocated at a 2:1 ratio to two groups: the SWD group and the control group. METHODS: Participants of the SWD group received SWD treatment, and participants of the control group received placebo SWD treatment for one session per day, 10 minutes per session, for no more than 14 days. Both groups were given standard care treatment. Primary outcome was the rate of clinical improvement according to a seven-category ordinal scale. Secondary outcomes included the rate of computed tomography (CT) improvement and the rate of potential adverse events. RESULTS: Clinical improvement occurred in 92.6% of patients in the SWD group by day 14 compared with 69.2% of patients in the control group (P=0.001). The Cox model indicated that the SWD group had a higher clinical improvement probability than the control group (hazard ratio: 3.045; 95% CI: 1.391-6.666; P=0.005). Similarly, CT improvement occurred in 85.2% of patients in the SWD group and 46.2% of patients in the control group respectively by day 14 (P=0.001). The Cox model indicated SWD group had a higher CT improvement probability than control group (hazard ratio: 3.720; 95% CI: 1.486-9.311; P=0.005). There was no significant difference in adverse events between the SWD group and the control group (2 of 27 [7.4%] SWD vs. 1 of 13 [7.7%] control, P=1.000), the most frequent of which were headache (1 of 27 [3.7%] SWD vs. 1 of 13 [7.7%] control patients) and dizziness (1 of 27 [3.7%] SWD vs. 0 of 13 [0%] control patients). CONCLUSIONS: SWD is a valid and reliable adjuvant therapy with a favorable safety profile for moderate COVID-19 patients. CLINICAL REHABILITATION IMPACT: Clinically relevant information is lacking regarding the efficacy and safety of SWD for patients with COVID-19. This study provides the first evidence that SWD is a promising adjuvant therapy for COVID-19.

Chicken Intestinal Microbiota Modulation of Resistance to Nephropathogenic Infectious Bronchitis Virus Infection Through IFN-I (preprint)

Background Mammalian intestinal microbiomes are necessary for antagonizing systemic viral infections. However, very few studies have identified whether poultry commensal bacteria play a crucial role in protecting against systemic viral infections. Nephropathogenic infectious bronchitis virus (IBV) is a pathogenic coronavirus that causes high morbidity and multiorgan infection tropism in chickens.Results In this study, we used broad-spectrum oral antibiotics (ABX) to treat specific pathogen free (SPF) chickens to deplete the microbiota before infection with nephropathogenic IBV to analyze the impact of microbiota on IBV infections in vivo. Depletion of the SPF chicken microbiota increases pathogenicity and viral burden following IBV infection. The gnotobiotic chicken infection model further demonstrated that intestinal microbes are resistant to nephropathogenic IBV infection. In addition, ABX-treated chickens showed a severe reduction in macrophage activation, impaired type I IFN production, and IFN-stimulated gene expression in peripheral blood mononuclear cells and the spleen. Lactobacillus isolated from SPF chickens could restore microbiota-depleted chicken macrophage activation and the IFNAR-dependent type I IFN response to limit IBV infection. Furthermore, exopolysaccharide metabolites of Lactobacillus spp. could induce IFN-β.Conclusions This study revealed the resistance mechanism of SPF chicken intestinal microbiota to nephropathogenic IBV infection, providing new ideas for preventing and controlling nephropathogenic IBV.

The spatiotemporal transmission dynamics of COVID-19 among multiple regions: a modeling study in Chinese provinces.

Current explosive outbreak of COVID-19 around the world is a complex spatiotemporal process with hidden interactions between viruses and humans. This study aims at clarifying the transmission patterns and the driving mechanism that contributed to the COVID-19 prevalence across the provinces of China. Thus, a new dynamical transmission model is established by an ordinary differential system. The model takes into account the hidden circulation of COVID-19 virus among/within humans, which incorporates the spatial diffusion of infection by parameterizing human mobility. Theoretical analysis indicates that the basic reproduction number is a unique epidemic threshold, which can unite infectivity in each region by human mobility and can totally determine whether COVID-19 proceeds among multiple regions. By validating the model with real epidemic data in China, it is found that (1) if without any intervention, COVID-19 would overrun China within three months, resulting in more than 1.1 billion clinical infections and 0.2 billion subclinical infections; (2) high frequency of human mobility can trigger COVID-19 diffusion across each province in China, no matter where the initial infection locates; (3) travel restrictions and other non-pharmaceutical interventions must be implemented simultaneously for disease control; and (4) infection sites in central and east (rather than west and northeast) of China would easily stimulate quick diffusion of COVID-19 in the whole country. Supplementary Information: The online version supplementary material available at 10.1007/s11071-021-07001-1.

Incidence, Etiology, and Environmental Risk Factors of Community-Acquired Pneumonia Requiring Hospitalization in China: A 3-Year, Prospective, Age-Stratified, Multicenter Case-Control Study.

Background: Community-acquired pneumonia (CAP) is a leading infectious cause of hospitalization and death worldwide. Knowledge about the incidence and etiology of CAP in China is fragmented. Methods: A multicenter study performed at 4 hospitals in 4 regions in China and clinical samples from CAP patients were collected and used for pathogen identification from July 2016 to June 2019. Results: A total of 1674 patients were enrolled and the average annual incidence of hospitalized CAP was 18.7 (95% confidence interval, 18.5-19.0) cases per 10000 people. The most common viral and bacterial agents found in patients were respiratory syncytial virus (19.2%) and Streptococcus pneumoniae (9.3%). The coinfections percentage was 13.8%. Pathogen distribution displayed variations within age groups as well as seasonal and regional differences. The severe acute respiratory syndrome coronavirus 2 was not detected. Respiratory virus detection was significantly positively correlated with air pollutants (including particulate matter ≤2.5 µm, particulate matter ≤10 µm, nitrogen dioxide, and sulfur dioxide) and significantly negatively correlated with ambient temperature and ozone content; bacteria detection was opposite. Conclusions: The hospitalized CAP incidence in China was higher than previously known. CAP etiology showed that differences in age, seasons, regions, and respiratory viruses were detected at a higher rate than bacterial infection overall. Air pollutants and temperature have an influence on the detection of pathogens.

The spatiotemporal transmission dynamics of COVID-19 among multiple regions: a modeling study in Chinese provinces

Current explosive outbreak of COVID-19 around the world is a complex spatiotemporal process with hidden interactions between viruses and humans. This study aims at clarifying the transmission patterns and the driving mechanism that contributed to the COVID-19 prevalence across the provinces of China. Thus, a new dynamical transmission model is established by an ordinary differential system. The model takes into account the hidden circulation of COVID-19 virus among/within humans, which incorporates the spatial diffusion of infection by parameterizing human mobility. Theoretical analysis indicates that the basic reproduction number is a unique epidemic threshold, which can unite infectivity in each region by human mobility and can totally determine whether COVID-19 proceeds among multiple regions. By validating the model with real epidemic data in China, it is found that (1) if without any intervention, COVID-19 would overrun China within three months, resulting in more than 1.1 billion clinical infections and 0.2 billion subclinical infections;(2) high frequency of human mobility can trigger COVID-19 diffusion across each province in China, no matter where the initial infection locates;(3) travel restrictions and other non-pharmaceutical interventions must be implemented simultaneously for disease control;and (4) infection sites in central and east (rather than west and northeast) of China would easily stimulate quick diffusion of COVID-19 in the whole country. Supplementary Information The online version supplementary material available at 10.1007/s11071-021-07001-1.

Ambient air pollution and low temperature associated with case fatality of COVID-19: A nationwide retrospective cohort study in China.

The evidence for the effects of environmental factors on COVID-19 case fatality remains controversial, and it is crucial to understand the role of preventable environmental factors in driving COVID-19 fatality. We thus conducted a nationwide cohort study to estimate the effects of environmental factors (temperature, particulate matter [PM2.5, PM10], sulfur dioxide [SO2], nitrogen dioxide [NO2], and ozone [O3]) on COVID-19 case fatality. A total of 71,808 confirmed COVID-19 cases were identified and followed up for their vital status through April 25, 2020. Exposures to ambient air pollution and temperature were estimated by linking the city- and county-level monitoring data to the residential community of each participant. For each participant, two windows were defined: the period from symptom onset to diagnosis (exposure window I) and the period from diagnosis date to date of death/recovery or end of the study period (exposure window II). Cox proportional hazards models were used to estimate the associations between these environmental factors and COVID-19 case fatality. COVID-19 case fatality increased in association with environmental factors for the two exposure windows. For example, each 10 µg/m3 increase in PM2.5, PM10, O3, and NO2 in window I was associated with a hazard ratio of 1.11 (95% CI 1.09, 1.13), 1.10 (95% CI 1.08, 1.13), 1.09 (95 CI 1.03, 1.14), and 1.27 (95% CI 1.19, 1.35) for COVID-19 fatality, respectively. A significant effect was also observed for low temperature, with a hazard ratio of 1.03 (95% CI 1.01, 1.04) for COVID-19 case fatality per 1°C decrease. Subgroup analysis indicated that these effects were stronger in the elderly, as well as in those with mild symptoms and living in Wuhan or Hubei. Overall, the sensitivity analyses also yielded consistent estimates. Short-term exposure to ambient air pollution and low temperature during the illness would play a nonnegligible part in causing case fatality due to COVID-19. Reduced exposures to high concentrations of PM2.5, PM10, O3, SO2, and NO2 and low temperature would help improve the prognosis and reduce public health burden.

Rapid One-Step Detection of Viral Particles Using an Aptamer-Based Thermophoretic Assay.

Rapid and sensitive identification of viral pathogens such as SARS-CoV-2 is a critical step to control the pandemic disease. Viral antigen detection can compete with gold-standard PCR-based nucleic acid diagnostics in terms of better reflection of viral infectivity and reduced risk of contamination from enzymatic amplification. Here, we report the development of a one-step thermophoretic assay using an aptamer and polyethylene glycol (PEG) for direct quantitative detection of viral particles. The assay relies on aptamer binding to the spike protein of SARS-CoV-2 and simultaneous accumulation of aptamer-bound viral particles in laser-induced gradients of temperature and PEG concentration. Using a pseudotyped lentivirus model, a limit of detection of ∼170 particles µL-1 (26 fM of the spike protein) is achieved in 15 min without the need of any pretreatment. As a proof of concept, the one-step thermophoretic assay is used to detect synthetic samples by spiking viral particles into oropharyngeal swabs with an accuracy of 100%. The simplicity, speed, and cost-effectiveness of this thermophoretic assay may expand the diagnostic tools for viral pathogens.

Population Movement, City Closure in Wuhan, and Geographical Expansion of the COVID-19 Infection in China in January 2020.

BACKGROUND: The unprecedented outbreak of corona virus disease 2019 (COVID-19) infection in Wuhan City has caused global concern; the outflow of the population from Wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city-closure measure to prevent its transmission considering the large amount of travel before the Chinese New Year. METHODS: Based on the daily reported new cases and the population-movement data between 1 and 31 January, we examined the effects of population outflow from Wuhan on the geographical expansion of the infection in other provinces and cities of China, as well as the impacts of the city closure in Wuhan using different closing-date scenarios. RESULTS: We observed a significantly positive association between population movement and the number of the COVID-19 cases. The spatial distribution of cases per unit of outflow population indicated that the infection in some areas with a large outflow of population might have been underestimated, such as Henan and Hunan provinces. Further analysis revealed that if the city-closure policy had been implemented 2 days earlier, 1420 (95% confidence interval, 1059-1833) cases could have been prevented, and if 2 days later, 1462 (1090-1886) more cases would have been possible. CONCLUSIONS: Our findings suggest that population movement might be one important trigger for the transmission of COVID-19 infection in China, and the policy of city closure is effective in controlling the epidemic.

Community evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through air.

BACKGROUND: Nine COVID-19 (Corona Virus Disease, 2019) cases were observed in one community in Guangzhou. All the cases lived in three vertically aligned units of one building sharing the same piping system, which provided one unique opportunity to examine the transmission mode of SARS-CoV-2. METHODS: We interviewed the cases on the history of travelling and close contact with the index patients. Respiratory samples from all the cases were collected for viral phylogenetic analyses. A simulation experiment in the building and a parallel control experiment in a similar building were then conducted to investigate the possibility of transmission through air. RESULTS: Index patients living in Apartment 15-b had a travelling history in Wuhan, and four cases who lived in Apartment 25-b and 27-b were subsequently diagnosed. Phylogenetic analyses showed that virus of all the patients were from the same strain of the virus. No close contacts between the index cases and other families indicated that the transmission might not occur through droplet and close contacts. Airflow detection and simulation experiment revealed that flushing the toilets could increase the speed of airflow in the pipes and transmitted the airflow from Apartment 15-b to 25-b and 27-b. Reduced exhaust flow rates in the infected building might have contributed to the outbreak. CONCLUSIONS: The outbreak of COVID-19 in this community could be largely explained by the transmission through air, and future efforts to prevent the infection should take the possibility of transmission through air into consideration. A disconnected drain pipe and exhaust pipe for toilet should be considered in the architectural design to help prevent possible virus spreading through the air.

A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing.

The outbreak of virus-induced infectious diseases poses a global public-health challenge. Nucleic acid amplification testing (NAAT) enables early detection of pandemic viruses and plays a vital role in preventing onward transmission. However, the requirement of skilled operators, expensive instrumentation, and biosafety laboratories has hindered the use of NAAT for screening and diagnosis of suspected patients. Here we report development of a fully automated centrifugal microfluidic system with sample-in-answer-out capability for sensitive, specific, and rapid viral nucleic acid testing. The release of nucleic acids and the subsequent reverse transcription loop-mediated isothermal amplification (RT-LAMP) were integrated into the reaction units of a microfluidic disc. The whole processing steps such as injection of reagents, fluid actuation by rotation, heating and temperature control, and detection of fluorescence signals were carried out automatically by a customized instrument. We validate the centrifugal microfluidic system using oropharyngeal swab samples spiked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) armored RNA particles. The estimated limit of detection for armored RNA particles is 2 copies per reaction, the throughput is 21 reactions per disc, and the assay sample-to-answer time is approximately 70 min. This enclosed and automated microfluidic system efficiently avoids viral contamination of aerosol, and can be readily adapted for virus detection outside the diagnostic laboratory. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at 10.1007/s11426-020-9800-6 and is accessible for authorized users.

Rehabilitation of patients with COVID-19.

INTRODUCTION: In 2020, due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), coronavirus disease (COVID-19) has become a pandemic. As of 11 August 2020, the cumulative number of confirmed cases worldwide had reached 19 million, with 700,000 reported deaths, indicating this pandemic's significant global impact. AREAS COVERED: We reviewed the application of rehabilitation therapy in the clinical treatment of COVID-19 patients. A systematic search was performed using PubMed, Springer, CNKI, and Wanfang Data of database up to 1 August 2020. The search terms included the English terms and their Chinese equivalents: 'COVID-19,' 'ARDS,' 'rehabilitation,' 'critically ill patients,' 'physiotherapy,' 'respiratory rehabilitation,' 'traditional Chinese medicine,' and 'psychotherapy.' EXPERT OPINION: Rehabilitation research concerning patients with COVID-19 remains ongoing. Rehabilitation guidance for such patients with COVID-19 is based on previous experience. However, as different patients have differing degrees of dysfunction, personalized plans need to be designed according to the patients' age, sex, lifestyle, hobbies, occupation, and physical conditions. The rapid development of remote devices that can monitor patients' real-time physical conditions post-discharge may encourage better adherence to rehabilitation training.

Predictive Model and Risk Factors for Case Fatality of COVID-19: A Cohort of 21,392 Cases in Hubei, China.

An increasing number of patients are being killed by coronavirus disease 2019 (COVID-19), however, risk factors for the fatality of COVID-19 remain unclear. A total of 21,392 COVID-19 cases were recruited in the Hubei Province of China between December 2019 and February 2020, and followed up until March 18, 2020. We adopted Cox regression models to investigate the risk factors for case fatality and predicted the death probability under specific combinations of key predictors. Among the 21,392 patients, 1,020 (4.77%) died of COVID-19. Multivariable analyses showed that factors, including age (≥60 versus <45 years, hazard ratio [HR] = 7.32; 95% confidence interval [CI], 5.42, 9.89), sex (male versus female, HR = 1.31; 95% CI, 1.15, 1.50), severity of the disease (critical versus mild, HR = 39.98; 95% CI, 29.52, 48.86), comorbidity (HR = 1.40; 95% CI, 1.23, 1.60), highest body temperature (>39°C versus <39°C, HR = 1.28; 95% CI, 1.09, 1.49), white blood cell counts (>10 × 109/L versus (4-10) × 109/L, HR = 1.69; 95% CI, 1.35, 2.13), and lymphocyte counts (<0.8 × 109/L versus (0.8-4) × 109/L, HR = 1.26; 95% CI, 1.06, 1.50) were significantly associated with case fatality of COVID-19 patients. Individuals of an older age, who were male, with comorbidities, and had a critical illness had the highest death probability, with 21%, 36%, 46%, and 54% within 1-4 weeks after the symptom onset. Risk factors, including demographic characteristics, clinical symptoms, and laboratory factors were confirmed to be important determinants of fatality of COVID-19. Our predictive model can provide scientific evidence for a more rational, evidence-driven allocation of scarce medical resources to reduce the fatality of COVID-19.

Epidemiological and clinical features of 200 hospitalized patients with corona virus disease 2019 outside Wuhan, China: A descriptive study.

BACKGROUND: The recent outbreak of coronavirus disease 2019 (COVID-19) has spread worldwide, with especially severe epidemics occurring in cities across China. OBJECTIVES: To report the epidemiological and clinical futures of the 200 patients infected with COVID-19 in Yichang, Hubei Province, China. STUDY DESIGN: 200 patients confirmed with COVID-19 in a designated hospital in Yichang from Jan 30 to Feb 8, 2020 were investigated retrospectively. The epidemiological data and clinical characteristics were collected. The data between the ICU patients and non-ICU patients were compared. The patients were followed up till Feb 26, 2020. RESULTS: Of the 200 hospitalized patients with COVID-19, 98 (49.0 %) were male, and the mean age was 55 years. Eighty-seven (43.5 %) had no linkage to Wuhan or contact history. Familial clustering was found in 34 patients. Sixtyfive (32.5 %) suffered from chronic diseases. The common symptoms included fever (171[85.5 %]), cough (116[58.0 %]), and fatigue (64[32 %]). Most patients had lymphopenia. One hundred and seventy-two (86 %) patients showed typical imaging findings of viral pneumonia. Most patients received antiviral, antibiotic, and corticosteroid treatment. Compared with the non-ICU patients, 29 (14.5 %) patients in the ICU were older and more likely to show dyspnea and complications including ARDS. As of Feb 26, 15 (51.7 %) patients in the ICU had died. CONCLUSIONS: The COVID-19 infection was of clustering onset and can cause severe respiratory disease and even death. The mortality of ICU patients with COVID-19 was considerably high.