Global age-structured spatial modeling for emerging infectious diseases like COVID-19.

Modeling the global dynamics of emerging infectious diseases (EIDs) like COVID-19 can provide important guidance in the preparation and mitigation of pandemic threats. While age-structured transmission models are widely used to simulate the evolution of EIDs, most of these studies focus on the analysis of specific countries and fail to characterize the spatial spread of EIDs across the world. Here, we developed a global pandemic simulator that integrates age-structured disease transmission models across 3,157 cities and explored its usage under several scenarios. We found that without mitigations, EIDs like COVID-19 are highly likely to cause profound global impacts. For pandemics seeded in most cities, the impacts are equally severe by the end of the first year. The result highlights the urgent need for strengthening global infectious disease monitoring capacity to provide early warnings of future outbreaks. Additionally, we found that the global mitigation efforts could be easily hampered if developed countries or countries near the seed origin take no control. The result indicates that successful pandemic mitigations require collective efforts across countries. The role of developed countries is vitally important as their passive responses may significantly impact other countries.

From Biowaste to Lab-Bench: Low-Cost Magnetic Iron Oxide Nanoparticles for RNA Extraction and SARS-CoV-2 Diagnostics.

The gold standard for diagnostics of SARS-CoV-2 (COVID-19) virus is based on real-time polymerase chain reaction (RT-PCR) using centralized PCR facilities and commercial viral RNA extraction kits. One of the key components of these kits are magnetic beads composed of silica coated magnetic iron oxide (Fe2O3 or Fe3O4) nanoparticles, needed for the selective extraction of RNA. At the beginning of the pandemic in 2019, due to a high demand across the world there were severe shortages of many reagents and consumables, including these magnetic beads required for testing for SARS-CoV-2. Laboratories needed to source these products elsewhere, preferably at a comparable or lower cost. Here, we describe the development of a simple, low-cost and scalable preparation of magnetic nanoparticles (MNPs) from biowaste and demonstrate their successful application in viral RNA extraction and the detection of COVID-19. These MNPs have a unique nanoplatelet shape with a high surface area, which are beneficial features, expected to provide improved RNA adsorption, better dispersion and processing ability compared with commercial spherical magnetic beads. Their performance in COVID-19 RNA extraction was evaluated in comparison with commercial magnetic beads and the results presented here showed comparable results for high throughput PCR analysis. The presented magnetic nanoplatelets generated from biomass waste are safe, low-cost, simple to produce in large scale and could provide a significantly reduced cost of nucleic acid extraction for SARS-CoV-2 and other DNA and RNA viruses.

A novel inhalable quercetin-alginate nanogel as a promising therapy for acute lung injury.

BACKGROUND: Acute lung injury (ALI), a severe health-threatening disease, has a risk of causing chronic pulmonary fibrosis. Informative and powerful evidence suggests that inflammation and oxidative stress play a central role in the pathogenesis of ALI. Quercetin is well recognized for its excellent antioxidant and anti-inflammatory properties, which showed great potential for ALI treatment. However, the application of quercetin is often hindered by its low solubility and bioavailability. Therefore, to overcome these challenges, an inhalable quercetin-alginate nanogel (QU-Nanogel) was fabricated, and by this special "material-drug" structure, the solubility and bioavailability of quercetin were significantly enhanced, which could further increase the activity of quercetin and provide a promising therapy for ALI. RESULTS: QU-Nanogel is a novel alginate and quercetin based "material-drug" structural inhalable nanogel, in which quercetin was stabilized by hydrogen bonding to obtain a "co-construct" water-soluble nanogel system, showing antioxidant and anti-inflammatory properties. QU-Nanogel has an even distribution in size of less than 100 nm and good biocompatibility, which shows a stronger protective and antioxidant effect in vitro. Tissue distribution results provided evidence that the QU-Nanogel by ultrasonic aerosol inhalation is a feasible approach to targeted pulmonary drug delivery. Moreover, QU-Nanogel was remarkably reversed ALI rats by relieving oxidative stress damage and acting the down-regulation effects of mRNA and protein expression of inflammation cytokines via ultrasonic aerosol inhalation administration. CONCLUSIONS: In the ALI rat model, this novel nanogel showed an excellent therapeutic effect by ultrasonic aerosol inhalation administration by protecting and reducing pulmonary inflammation, thereby preventing subsequent pulmonary fibrosis. This work demonstrates that this inhalable QU-Nanogel may function as a promising drug delivery strategy in treating ALI.

Rapid and Accurate Detection of SARS Coronavirus 2 by Nanopore Amplicon Sequencing.

Objective: We aimed to evaluate the performance of nanopore amplicon sequencing detection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples. Method: We carried out a single-center, prospective cohort study in a Wuhan hospital and collected a total of 86 clinical samples, including 54 pharyngeal swabs, 31 sputum samples, and 1 fecal sample, from 86 patients with coronavirus disease 2019 (COVID-19) from Feb 20 to May 15, 2020. We performed parallel detection with nanopore-based genome amplification and sequencing (NAS) on the Oxford Nanopore Technologies (ONT) minION platform and routine reverse transcription quantitative polymerase chain reaction (RT-qPCR). In addition, 27 negative control samples were detected using the two methods. The sensitivity and specificity of NAS were evaluated and compared with those of RT-qPCR. Results: The viral read number and reference genome coverage were both significantly different between the two groups of samples, and the latter was a better indicator for SARS-CoV-2 detection. Based on the reference genome coverage, NAS revealed both high sensitivity (96.5%) and specificity (100%) compared with RT-qPCR (80.2 and 96.3%, respectively), although the samples had been stored for half a year before the detection. The total time cost was less than 15 h, which was acceptable compared with that of RT-qPCR (∼2.5 h). In addition, the reference genome coverage of the viral reads was in line with the cycle threshold value of RT-qPCR, indicating that this number could also be used as an indicator of the viral load in a sample. The viral load in sputum might be related to the severity of the infection, particularly in patients within 4 weeks after onset of clinical manifestations, which could be used to evaluate the infection. Conclusion: Our results showed the high sensitivity and specificity of the NAS method for SARS-CoV-2 detection compared with RT-qPCR. The sequencing results were also used as an indicator of the viral load to display the viral dynamics during infection. This study proved the wide application prospect of nanopore sequencing detection for SARS-CoV-2 and may more knowledge about the clinical characteristics of COVID-19.

A Confirmed Case of SARS-CoV-2 Pneumonia With Negative Routine Reverse Transcriptase-Polymerase Chain Reaction and Virus Variation in Guangzhou, China.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia is a newly recognized disease, and its diagnosis is primarily confirmed by routine reverse transcriptase -polymerase chain reaction (RT-PCR) detection of SARS-CoV-2. METHODS: However, we report a confirmed case of SARS-CoV-2 pneumonia with a negative routine RT-PCR. RESULTS: This case was finally diagnosed by nanopore sequencing combined with antibody of SARS-CoV-2. Simultaneously, the ORF and NP gene variations of SARS-CoV-2 were found. CONCLUSIONS: This case highlighted that false-negative results could be present in routine RT-PCR diagnosis, especially with virus variation. Currently, nanopore pathogen sequencing and antibody detection have been found to be effective in clinical diagnosis.

Modelling the epidemic dynamics of COVID-19 with consideration of human mobility.

So far COVID-19 has resulted in mass deaths and huge economic losses across the world. Various measures such as quarantine and social distancing have been taken to prevent the spread of this disease. These prevention measures have changed the transmission dynamics of COVID-19 and introduced new challenges for epidemic modelling and prediction. In this paper, we study a novel disease spreading model with two important aspects. First, the proposed model takes the quarantine effect of confirmed cases on transmission dynamics into account, which can better resemble the real-world scenario. Second, our model incorporates two types of human mobility, where the intra-region human mobility is related to the internal transmission speed of the disease in the focal area and the inter-region human mobility reflects the scale of external infectious sources to a focal area. With the proposed model, we use the human mobility data from 24 cities in China and 8 states in the USA to analyse the disease spreading patterns. The results show that our model could well fit/predict the reported cases in both countries. The predictions and findings shed light on how to effectively control COVID-19 by managing human mobility behaviours.

Longitudinal virological changes and underlying pathogenesis in hospitalized COVID-19 patients in Guangzhou, China.

Prolonged viral RNA shedding and recurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in coronavirus disease 2019 (COVID-19) patients have been reported. However, the clinical outcome and pathogenesis remain unclear. In this study, we recruited 43 laboratory-confirmed COVID-19 patients. We found that prolonged viral RNA shedding or recurrence mainly occurred in severe/critical patients (P<0.05). The average viral shedding time in severe/critical patients was more than 50 days, and up to 100 days in some patients, after symptom onset. However, chest computed tomography gradually improved and complete absorption occurred when SARS-CoV-2 RT-PCR was still positive, but specific antibodies appeared. Furthermore, the viral shedding time significantly decreased when the A1,430G or C12,473T mutation occurred (P<0.01 and FDR<0.01) and increased when G227A occurred (P<0.05 and FDR<0.05). High IL1R1, IL1R2, and TNFRSF21 expression in the host positively correlated with viral shedding time (P<0.05 and false discovery rate <0.05). Prolonged viral RNA shedding often occurs but may not increase disease damage. Prolonged viral RNA shedding is associated with viral mutations and host factors.

Monitoring Crop Growth During the Period of the Rapid Spread of COVID-19 in China by Remote Sensing.

The status of crop growth under the influence of COVID-19 is an important information for evaluating the current food security in China. This article used the cloud computing platform of Google Earth Engine, to access and analyze Sentinel-2, MODIS, and other multisource remote sensing data in the last five years to monitor the growth of crops in China, especially in Hubei province, during the period of the rapid spread of COVID-19 (i.e., from late January to mid-March 2020), and compared with the growth over the same period under similar climate conditions in the past four years. We further analyzed the indirect effects of COVID-19 on crop growth. The results showed that: the area of the crops with better growth (51%) was much more than that with worse growth (22%); the crops with better and worse growth were mainly distributed in the North China Plain (the main planting areas of winter wheat in China) and the South China regions (such as Guangxi, Guangdong province), respectively. The area of the crops with a similar growth occupied 27%. In Hubei province, the area of the crops with better growth (61%) was also more than that with worse growth (27%). It was found that there was no obvious effect from COVID-19 on the overall growth of crops in China during the period from late January to mid-March 2020 and the growth of crops was much better than that during the same period in previous years. The findings in this study are helpful in evaluating the impact of the COVID-19 on China's agriculture, which are conducive to serve the relevant agricultural policy formulation and to ensure food security.

[Moxibustion therapy in prevention and treatment of coronavirus disease 2019 (COVID-19): construction and application of non-contact diagnosis and treatment mode].

OBJECTIVE: To establish and promote the non-contact doctor-patient interactive diagnosis and treatment mode based on mobile internet for the treatment of coronavirus disease 2019 (COVID-19) with moxibustion therapy, and to observe the feasibility and effectiveness of the model in the pandemic. METHODS: A total of 43 first-line medical staff and 149 suspected and confirmed cases with COVID-19 [18 cases in medical observation period, 17 cases of mild type (cold dampness and stagnation in the lung), 24 cases of ordinary type (cold-dampness accumulated in the lung) and 90 cases in recovery period (qi deficiency of spleen and lung)] were included. A non-contact doctor-patient interactive diagnosis and treatment platform was established for the treatment of COVID-19 with indirect moxibustion plaster based on mobile internet. By the platform, the patients were instructed to use indirect moxibustion plaster in treatment. For the first-line medical staff and patients in the medical observation period, Zusanli (ST 36), Qihai (CV 6) and Zhongwan (CV 12) were selected. For the mild cases (cold dampness and stagnation in the lung) and the cases of ordinary type (cold-dampness accumulated in the lung), Hegu (LI 4), Taichong (LR 3), Zusanli (ST 36) and Guanyuan (CV 4) were selected. In the recovery period (qi deficiency of spleen and lung), Dazhui (GV 14), Feishu (BL 13), Geshu (BL 17), Zusanli (ST 36) and Kongzui (LU 6) were used. The treatment was given once daily for 40 min each time. The intervention lasted for 10 days. After intervention, the infection rate and the improvement in the symptoms and psychological status of COVID-19 were observed in clinical first-line medical staff and COVID-19 patients. RESULTS: In 10 days of intervention with indirect moxibustion plaster, there was "zero" infection among medical staff. Of 43 first-line physicians and nurses, 33 cases had some physical symptoms and psychological discomforts, mainly as low back pain, poor sleep and anxiety. After treatment, regarding the improvements in the symptoms and psychological discomforts, the effective rate was 78.8% (26/33) and the curative rate was 36.4% (12/33). Regarding the improvements in psychological discomforts, the effective rate was 58.3% (14/24) and the curative rate was 37.5 (9/24). Of 149 patients, 133 cases had the symptoms and psychological discomforts. After treatment, regarding the improvements in the symptoms and psychological discomforts, the effective rate was 81.2% (108/133) and the curative rate was 34.6% (46/133). Regarding the improvements in psychological discomforts, the effective rate was 76.5% (52/68) and the curative rate was 57.4 % (39/68). CONCLUSION: It is feasible to apply the indirect moxibustion plaster technique based on mobile internet to the treatment COVID-19. This mode not only relieves the symptoms such as cough and fatigue, improves psychological state, but also possibly prevents the first-line medical staff from COVID-19.

A combined abiotic oxidation-precipitation process for rapid As removal from high-As(III)-Mn(II) acid mine drainage and low As-leaching solid products

A combination process of Fenton-like and catalytic Mn(II) oxidation via molecular oxygen-induced abio-oxidation of As(III)-Mn(II)-rich acid mine drainage (AMD) is developed to rapidly and efficiently remove As and obtain low As-leaching solids in this study. The effect of pH, temperature, oxygen flow rate and neutralization reagent on As removal was investigated. The results showed that pH was important to As removal efficiency, which achieved maximum in 0.25-2 h, but decreased from ∼100 % to ∼92.6 % with the increase of pH 5-9. pH, temperature and oxygen flow rate played key roles in As(III) oxidation. The increase of As(III) oxidized from 16.8 to 67.1% to 98.6-99.0 % occurred as increasing the pH 5-9, 25-95 °C and oxygen flow rate of 0-2.4 L min-1. NaOH or Ca(OH)2 as base was less important to As removal. The mechanism involved Fenton-like reaction between Fe(II) and O2 for produced Fe(III) (oxy)hydroxide association with As(III + V) and Mn(II), catalytic Mn(II) oxidation for the formation of Mn(III, IV) oxides, and further As(III) oxidation by Mn(III, IV) oxides. As-bearing six-line ferrihydrite was the main solid product for low As-leaching fixation. pH 8, 95 °C and oxygen flow rate of 1.6 L min-1 were optimal for As removal.