Role of wastewater treatment in COVID-19 control

The International Water Association (IWA) initiated a Task Force in April 2020 to serve as a leadership team within IWA whose role is to keep abreast and communicate the emerging science, technology, and applications for understanding the impact and the ability to respond to the COVID-19 pandemic and specifically designed for water professionals and industries. Expertise was nominated across the world with the purpose of collectively providing the water sector with knowledge products for the guidance on the control of COVID-19 and other viruses. This review paper developed by a working group of the IWA Task Force focuses on the control of COVID-19. The purpose of this review paper is to provide an understanding of existing knowledge with regards to COVID-19 and provide the necessary guidance of risk mitigation based on currently available knowledge of viruses in wastewater. This review paper considered various scenarios for both the developed world and the developing world and provided recommendations for managing risk. The review paper serves to pool the knowledge with regards to the pandemic and in relation to other viruses. The IWA Task Team envisage that this review paper provides the necessary guidance to the global response to the ongoing pandemic.

Estimating infection fatality risk and ascertainment bias of COVID-19 in Osaka, Japan from February 2020 to January 2022.

The present study aimed to estimate the infection fatality risk (IFR) and ascertainment bias of SARS-CoV-2 for six epidemic waves in Japan from February 2020 to January 2022. We used two types of datasets: (i) surveillance-based datasets containing the cumulative numbers of confirmed cases and deaths in each epidemic wave and (ii) seroepidemiological datasets conducted in a serial cross-sectional manner. Smoothing spline function was employed to reconstruct the age-specific cumulative incidence of infection. We found that IFR was highest during the first wave, and the second highest during the fourth wave, caused by the Alpha variant. Once vaccination became widespread, IFR decreased considerably among adults aged 40 years plus during the fifth wave caused by the Delta variant, although the epidemic size of fifth wave was the largest before the Omicron variant emerged. We also found that ascertainment bias was relatively high during the first and second waves and, notably, RT-PCR testing capacity during these early periods was limited. Improvements in the ascertainment were seen during the third and fourth waves. Once the Omicron variant began spreading, IFR diminished while ascertainment bias was considerably elevated.

How Do Repeated Viewings in Forest Landscapes Influence Young People's Visual Behaviors and Cognitive Evaluations?

BACKGROUND: With the spread of the COVID-19 epidemic, it has gradually become normal to periodically visit and enjoy forest landscape resources in the suburbs of cities. For designers and managers of forest landscapes, exploring change in the visual behaviors and cognitive evaluations of people who repeatedly view forest landscapes and the characteristics of this change will aid the design and sustainable utilization of forest landscape resources in the suburbs of cities. PURPOSE: From the perspective of users' preferences for forest landscape space, this study explored the changes in visual behavior characteristics and psychological preference characteristics for individuals who repeatedly view forest landscapes and their drivers under different preferences. METHODS: This study collected data from 52 graduate and undergraduate students. We used a difference test to compare the differences in the visual behavior coincidence degree and the changes in psychological evaluations; a descriptive statistical analysis to explore young peoples' likes and dislikes of landscape elements; and Spearman correlation analysis to explore the correlation between the psychological evaluations and visual behaviors. MAIN RESULTS: 1. At the second viewing, the participants' regression behavior tended to decrease for various spaces, and they were more inclined to view areas that they had not viewed before. In addition, at the second viewing, the degree of fixation behavior coincidence was generally low, and there were obvious differences across spaces; 2. The participants' feature evaluations and comprehensive evaluations for landscapes did not change significantly with their increased familiarity with the spaces; 3. There was a significant positive correlation between the participants' psychological evaluations of landscape stimuli and the degree of fixation coincidence when viewing the spaces, among which the rate of distant clarity and the degree of fixation behavior coincidence were significantly and positively correlated. Meanwhile, at the second viewing, the number of favorite elements in the lookout space, which belongs to high-preference spaces, noticeably increased.

The city-wide full-scale interactive application of sewage surveillance programme for assisting real-time COVID-19 pandemic control - A case study in Hong Kong.

The paper discusses the implementation of Hong Kong's tailor-made sewage surveillance programme led by the Government, which has demonstrated how an efficient and well-organized sewage surveillance system can complement conventional epidemiological surveillance to facilitate the planning of intervention strategies and actions for combating COVID-19 pandemic in real-time. This included the setting up of a comprehensive sewerage network-based SARS-CoV-2 virus surveillance programme with 154 stationary sites covering 6 million people (or 80 % of the total population), and employing an intensive monitoring programme to take samples from each stationary site every 2 days. From 1 January to 22 May 2022, the daily confirmed case count started with 17 cases per day on 1 January to a maximum of 76,991 cases on 3 March and dropped to 237 cases on 22 May. During this period, a total of 270 "Restriction-Testing Declaration" (RTD) operations at high-risk residential areas were conducted based on the sewage virus testing results, where over 26,500 confirmed cases were detected with a majority being asymptomatic. In addition, Compulsory Testing Notices (CTN) were issued to residents, and the distribution of Rapid Antigen Test kits was adopted as alternatives to RTD operations in areas of moderate risk. These measures formulated a tiered and cost-effective approach to combat the disease in the local setting. Some ongoing and future enhancement efforts to improve efficacy are discussed from the perspective of wastewater-based epidemiology. Forecast models on case counts based on sewage virus testing results were also developed with R2 of 0.9669-0.9775, which estimated that up to 22 May 2022, around 2,000,000 people (~67 % higher than the total number of 1,200,000 reported to the health authority, due to various constraints or limitations) had potentially contracted the disease, which is believed to be reflecting the real situation occurring in a highly urbanized metropolis like Hong Kong.

Cov-TransNet: Dual branch fusion network with transformer for COVID-19 infection segmentation.

Segmentation of COVID-19 infection is a challenging task due to the blurred boundaries and low contrast between the infected and the non-infected areas in COVID-19 CT images, especially for small infection regions. COV-TransNet is presented to achieve high-precision segmentation of COVID-19 infection regions in this paper. The proposed segmentation network is composed of the auxiliary branch and the backbone branch. The auxiliary branch network adopts transformer to provide global information, helping the convolution layers in backbone branch to learn specific local features better. A multi-scale feature attention module is introduced to capture contextual information and adaptively enhance feature representations. Specially, a high internal resolution is maintained during the attention calculation process. Moreover, feature activation module can effectively reduce the loss of valid information during sampling. The proposed network can take full advantage of different depth and multi-scale features to achieve high sensitivity for identifying lesions of varied sizes and locations. We experiment on several datasets of the COVID-19 lesion segmentation task, including COVID-19-CT-Seg, UESTC-COVID-19, MosMedData and COVID-19-MedSeg. Comprehensive results demonstrate that COV-TransNet outperforms the existing state-of-the-art segmentation methods and achieves better segmentation performance for multi-scale lesions.

The impact of COVID-19 non-pharmaceutical interventions on HIV care continuum in China: An interrupted time series analysis.

Background: China implemented strict non-pharmaceutical interventions to contain COVID-19 at the early stage. We aimed to evaluate the impact of COVID-19 on HIV care continuum in China. Methods: Aggregated data on HIV care continuum between 1 January 2017 and 31 December 2020 were collected from centers for disease control and prevention at different levels and major infectious disease hospitals in various regions in China. We used interrupted time series analysis to characterize temporal trend in weekly numbers of HIV post-exposure prophylaxis (PEP) prescriptions, HIV tests, HIV diagnoses, median time intervals between HIV diagnosis and antiretroviral therapy (ART) initiation (time intervals, days), ART initiations, mean CD4+ T cell counts at ART initiation (CD4 counts, cells/µL), ART collections, and missed visits for ART collection, before and after the implementation of massive NPIs (23 January to 7 April 2020). We used Poisson segmented regression models to estimate the immediate and long-term impact of NPIs on these outcomes. Findings: A total of 16,780 PEP prescriptions, 1,101,686 HIV tests, 69,659 HIV diagnoses, 63,409 time intervals and ART initiations, 61,518 CD4 counts, 1,528,802 ART collections, and 6656 missed visits were recorded during the study period. The majority of outcomes occurred in males (55·3-87·4%), 21-50 year olds (51·7-90·5%), Southwestern China (38·2-82·0%) and heterosexual transmission (47·9-66·1%). NPIs was associated with 71·5% decrease in PEP prescriptions (IRR 0·285; 95% CI 0·192-0·423), 36·1% decrease in HIV tests (0·639, 0·497-0·822), 32·0% decrease in HIV diagnoses (0·680, 0·511-0·904), 59·3% increase in time intervals (1·593, 1·270-1·997) and 17·4% decrease in CD4 counts (0·826, 0·746-0·915) in the first week during NPIs. There was no marked change in the number of ART initiations, ART collections and missed visits during the NPIs. By the end of 2020, the number of HIV tests, HIV diagnoses, time intervals, ART initiations, and CD4 counts reached expected levels, but the number of PEP prescriptions (0·523, 0·394-0·696), ART collections (0·720, 0·595-0·872), and missed visits (0·137, 0·086-0·220) were still below expected levels. With the ease of restrictions, PEP prescriptions (slope change 1·024/week, 1·012-1·037), HIV tests (1·016/week, 1·008-1·026), and CD4 counts (1·005/week, 1·001-1·009) showed a significant increasing trend. Interpretation: HIV care continuum in China was affected by the COVID-19 NPIs at various levels. Preparedness and efforts to maintain the HIV care continuum during public health emergencies should leverage collaborations between stakeholders. Funding: Natural Science Foundation of China.

Mapping Population Distribution with High Spatiotemporal Resolution in Beijing Using Baidu Heat Map Data

Population distribution data with high spatiotemporal resolution are of significant value and fundamental to many application areas, such as public health, urban planning, environmental change, and disaster management. However, such data are still not widely available due to the limited knowledge of complex human activity patterns. The emergence of location-based service big data provides additional opportunities to solve this problem. In this study, we integrated ambient population data, nighttime light data, and building volume data;innovatively proposed a spatial downscaling framework for Baidu heat map data during work time and sleep time;and mapped the population distribution with high spatiotemporal resolution (i.e., hourly, 100 m) in Beijing. Finally, we validated the generated population distribution maps with high spatiotemporal resolution using the highest-quality validation data (i.e., mobile signaling data). The relevant results indicate that our proposed spatial downscaling framework for both work time and sleep time has high accuracy, that the distribution of the population in Beijing on a regular weekday shows 'centripetal centralization at daytime, centrifugal dispersion at night';spatiotemporal variation characteristics, that the interaction between the purpose of residents' activities and the spatial functional differences leads to the spatiotemporal evolution of the population distribution, and that China's 'surgical control and dynamic zero COVID-19';epidemic policy was strongly implemented. In addition, our proposed spatial downscaling framework can be transferred to other regions, which is of value for governmental emergency measures and for studies about human risks to environmental issues.

It is time to improve the acceptance of COVID-19 vaccines among people with chronic diseases: A systematic review and meta-analysis.

This study aims to investigated COVID-19 vaccine acceptance among people with chronic diseases and the factors correlating with their vaccination hesitancy. The articles were searched in PubMed, Ovid, EMBASE, and web of science databases between December 2019 and October 2022. Cross-sectional studies, including the acceptance of the COVID-19 vaccine by patients with chronic diseases (≥18 years old), were included in this study. The outcomes included the proportion and 95% confidence interval (95% CI) of chronic disease patients willing to be vaccinated and the odds ratio (OR) and 95% CI of correlating factors. The source of heterogeneity was analyzed through meta-regression and subgroup analysis. We included 31 studies involving 57 875 patients with chronic disease. The overall COVID-19 vaccine acceptance among patients with chronic disease was 0.65 (95% CI, 0.59-0.72). The acceptance among the elderly patients was 0.53 (95% CI, 0.26-0.80). South America had the highest COVID-19 vaccine acceptance rate and Asia the lowest, while on a country level, the United Kingdom had the highest acceptance rate among patients with chronic diseases. People with rheumatic immune diseases had the lowest rate of COVID-19 vaccine acceptance. Concerns about vaccine safety had a statistically different effect on acceptance. Overall, the health systems ought to focus on educating specific groups of individuals on the benefits of COVID-19 vaccination and addressing safety concerns.

COVID-19 cases with a contact history: A modeling study of contact history-stratified data in Japan.

The purpose of the present study was to develop a transmission model of COVID-19 cases with and without a contact history to understand the meaning of the proportion of infected individuals with a contact history over time. We extracted epidemiological information regarding the proportion of coronavirus disease 2019 (COVID-19) cases with a contact history and analyzed incidence data stratified by the presence of a contact history in Osaka from January 15 to June 30, 2020. To clarify the relationship between transmission dynamics and cases with a contact history, we used a bivariate renewal process model to describe transmission among cases with and without a contact history. We quantified the next-generation matrix as a function of time; thus, the instantaneous (effective) reproduction number was calculated for different periods of the epidemic wave. We objectively interpreted the estimated next-generation matrix and replicated the proportion of cases with a contact p(t) over time, and we examined the relevance to the reproduction number. We found that p(t) does not take either the maximum or minimum value at a threshold level of transmission with R(t)=1.0. With R(t) < 1 (subcritical level), p(t) was a decreasing function of R(t). Qualitatively, the minimum p(t) was seen in the domain with R(t) > 1. An important future implication for use of the proposed model is to monitor the success of ongoing contact tracing practice. A decreasing signal of p(t) reflects the increasing difficulty of contact tracing. The present study findings indicate that monitoring p(t) would be a useful addition to surveillance.

Protection against SARS-CoV-2 BA.4 and BA.5 subvariants via vaccination and natural infection: A modeling study.

With continuing emergence of new SARS-CoV-2 variants, understanding the proportion of the population protected against infection is crucial for public health risk assessment and decision-making and so that the general public can take preventive measures. We aimed to estimate the protection against symptomatic illness caused by SARS-CoV-2 Omicron variants BA.4 and BA.5 elicited by vaccination against and natural infection with other SARS-CoV-2 Omicron subvariants. We used a logistic model to define the protection rate against symptomatic infection caused by BA.1 and BA.2 as a function of neutralizing antibody titer values. Applying the quantified relationships to BA.4 and BA.5 using two different methods, the estimated protection rate against BA.4 and BA.5 was 11.3% (95% confidence interval [CI]: 0.01-25.4) (method 1) and 12.9% (95% CI: 8.8-18.0) (method 2) at 6 months after a second dose of BNT162b2 vaccine, 44.3% (95% CI: 20.0-59.3) (method 1) and 47.3% (95% CI: 34.1-60.6) (method 2) at 2 weeks after a third BNT162b2 dose, and 52.3% (95% CI: 25.1-69.2) (method 1) and 54.9% (95% CI: 37.6-71.4) (method 2) during the convalescent phase after infection with BA.1 and BA.2, respectively. Our study indicates that the protection rate against BA.4 and BA.5 are significantly lower compared with those against previous variants and may lead to substantial morbidity, and overall estimates were consistent with empirical reports. Our simple yet practical models enable prompt assessment of public health impacts posed by new SARS-CoV-2 variants using small sample-size neutralization titer data to support public health decisions in urgent situations.

A rapid, high-throughput, and sensitive PEG-precipitation method for SARS-CoV-2 wastewater surveillance.

The effective application of wastewater surveillance is dependent on testing capacity and sensitivity to obtain high spatial resolution testing results for a timely targeted public health response. To achieve this purpose, the development of rapid, high-throughput, and sensitive virus concentration methods is urgently needed. Various protocols have been developed and implemented in wastewater surveillance networks so far, however, most of them lack the ability to scale up testing capacity or cannot achieve sufficient sensitivity for detecting SARS-CoV-2 RNA at low prevalence. In the present study, using positive raw wastewater in Hong Kong, a PEG precipitation-based three-step centrifugation method was developed, including low-speed centrifugation for large particles removal and the recovery of viral nucleic acid, and medium-speed centrifugation for the concentration of viral nucleic acid. This method could process over 100 samples by two persons per day to reach the process limit of detection (PLoD) of 3286 copies/L wastewater. Additionally, it was found that the testing capacity could be further increased by decreasing incubation and centrifugation time without significantly influencing the method sensitivity. The entire procedure uses ubiquitous reagents and instruments found in most laboratories to obtain robust testing results. This high-throughput, cost-effective, and sensitive tool will promote the establishment of nearly real-time wastewater surveillance networks for valuable public health information.

Myopia progression and associated factors of refractive status in children and adolescents in Tibet and Chongqing during the COVID-19 pandemic.

Objectives: To investigate myopia progression and associated factors of refractive status among children and adolescents in Tibet and Chongqing in China during the COVID-19 pandemic. Methods: A population-based cross-sectional study was conducted to compare rates of myopia and high myopia, axial length (AL), spherical equivalent (SE), outdoor activity time, digital device use, and frequency of visual examinations for children and adolescents affected by myopia in Chongqing and Tibet in 2021. Results: A total of 2,303 students from Chongqing and 1,687 students from Tibet were examined. The overall prevalence of myopia and high myopia in these two groups were 53.80 and 7.04% vs. 43.86 and 1.30%, respectively in each case. The Chongqing students had a longer AL than the group from Tibet (23.95 vs. 23.40 mm, respectively; p < 0.001). The mean SE of the students with myopic parents in Tibet was lower than that of the students in Chongqing with myopic parents (-2.57 ± 2.38 diopters (D) vs. -2.30 ± 2.34 D, respectively) (p < 0.001). Conversely, the mean SE of the students from urban areas in Chongqing was lower than that of the students in Tibet (-2.26 ± 2.25 D vs. -1.75 ± 1.96 D, respectively; p < 0.001). The Chongqing students exhibited lower SE (-2.44 ± 2.22 D) than their Tibetan counterparts (mean SE: -1.78 ± 1.65 D (p = 0.0001) when spending more than 2.5 h outdoors. For example, 61.35% of the students in Tibet spent more than 2.5 h outdoors daily, compared with 43.04% of the students in Chongqing. Correspondingly, the proportion of students using digital devices in Tibet (64.43%) was lower than that in Chongqing (100%). For the latter, 38.62% of the students in Chongqing spent more than 2.5 h online using digital devices compared to 10.49% of the students in Tibet. Greater monitoring of visual status was observed for the Chongqing students (mean SE: -1.90 ± 1.98 D) compared with students in Tibet (mean SE: -2.68 ± 1.85 D) (p = 0.0448), with the frequency of optimal examinations being every 6 months. Outdoor activity time was identified as a common risk factor for myopia in both of the populations examined, with odds ratios (ORs) of 1.84 (95% CI: 1.79-1.90) in Chongqing and 0.84 (95% CI: 0.73-0.96) in Tibet. Digital screen time was associated with myopia and high myopia in Chongqing, with ORs of 1.15 (95% CI: 1.08-1.22) and 1.06 (95% CI: 0.94-1.77), respectively. Digital screen time was also found to be a risk factor for high myopia in Tibet (OR: 1.21, 95% CI: 0.77-1.61). The type of digital devices used was also associated with myopia and high myopia in Tibet (OR: 1.33, 95% CI: 1.06-1.68 and OR: 1.49, 95% CI: 0.84-2.58, respectively). Finally, examination frequency was found to correlate with high myopia in the Tibet group (OR: 1.79, 95% CI: 0.66-2.71). Conclusion: Based on our data, we observed that the prevalence of refractive errors in children and adolescents was significantly lower in Tibet than in Chongqing. These results are potentially due to prolonged outdoor activity time, and the type and time of use for digital devices that characterize the group of children and adolescents from Tibet. It is recommended that parents and children in Chongqing would benefit from increased awareness regarding myopia progression and its prevention.

Myopia progression and associated factors of refractive status in children and adolescents in Tibet and Chongqing during the COVID-19 pandemic

Objectives To investigate myopia progression and associated factors of refractive status among children and adolescents in Tibet and Chongqing in China during the COVID-19 pandemic. Methods A population-based cross-sectional study was conducted to compare rates of myopia and high myopia, axial length (AL), spherical equivalent (SE), outdoor activity time, digital device use, and frequency of visual examinations for children and adolescents affected by myopia in Chongqing and Tibet in 2021. Results A total of 2,303 students from Chongqing and 1,687 students from Tibet were examined. The overall prevalence of myopia and high myopia in these two groups were 53.80 and 7.04% vs. 43.86 and 1.30%, respectively in each case. The Chongqing students had a longer AL than the group from Tibet (23.95 vs. 23.40 mm, respectively;p < 0.001). The mean SE of the students with myopic parents in Tibet was lower than that of the students in Chongqing with myopic parents (−2.57 ± 2.38 diopters (D) vs. −2.30 ± 2.34 D, respectively) (p < 0.001). Conversely, the mean SE of the students from urban areas in Chongqing was lower than that of the students in Tibet (−2.26 ± 2.25 D vs. −1.75 ± 1.96 D, respectively;p < 0.001). The Chongqing students exhibited lower SE (−2.44 ± 2.22 D) than their Tibetan counterparts (mean SE: −1.78 ± 1.65 D (p = 0.0001) when spending more than 2.5 h outdoors. For example, 61.35% of the students in Tibet spent more than 2.5 h outdoors daily, compared with 43.04% of the students in Chongqing. Correspondingly, the proportion of students using digital devices in Tibet (64.43%) was lower than that in Chongqing (100%). For the latter, 38.62% of the students in Chongqing spent more than 2.5 h online using digital devices compared to 10.49% of the students in Tibet. Greater monitoring of visual status was observed for the Chongqing students (mean SE: −1.90 ± 1.98 D) compared with students in Tibet (mean SE: −2.68 ± 1.85 D) (p = 0.0448), with the frequency of optimal examinations being every 6 months. Outdoor activity time was identified as a common risk factor for myopia in both of the populations examined, with odds ratios (ORs) of 1.84 (95% CI: 1.79–1.90) in Chongqing and 0.84 (95% CI: 0.73–0.96) in Tibet. Digital screen time was associated with myopia and high myopia in Chongqing, with ORs of 1.15 (95% CI: 1.08–1.22) and 1.06 (95% CI: 0.94–1.77), respectively. Digital screen time was also found to be a risk factor for high myopia in Tibet (OR: 1.21, 95% CI: 0.77–1.61). The type of digital devices used was also associated with myopia and high myopia in Tibet (OR: 1.33, 95% CI: 1.06–1.68 and OR: 1.49, 95% CI: 0.84–2.58, respectively). Finally, examination frequency was found to correlate with high myopia in the Tibet group (OR: 1.79, 95% CI: 0.66–2.71). Conclusion Based on our data, we observed that the prevalence of refractive errors in children and adolescents was significantly lower in Tibet than in Chongqing. These results are potentially due to prolonged outdoor activity time, and the type and time of use for digital devices that characterize the group of children and adolescents from Tibet. It is recommended that parents and children in Chongqing would benefit from increased awareness regarding myopia progression and its prevention.

Fully Automated CRISPR-LAMP Platform for SARS-CoV-2 Delta and Omicron Variants.

Integrated clustered regularly interspaced short palindromic repeat (CRISPR)-loop-mediated amplification (LAMP) technology is of great importance in CRISPR-based diagnostic systems, which urgently needs to be developed to improve diagnostic accuracy. A labor-free, contamination-free, and fully automated droplet manipulation platform for the CRISPR-LAMP technology has not been developed before. Herein, we propose a fully automated CRISPR-LAMP platform, which can precisely manipulate the CRISPR-LAMP droplet and perform combined reactions with high sensitivity and specificity. SARS-CoV-2 Spike T478K, D614G, P681R, and P681H mutations, typical point mutations of B.1.617.2 (Delta) and Omicron variants, are monitored with this platform with a detection limit of 102 copies/µL. Allele discrimination between the mutants and wild type is significant with the designed one/two-mismatch CRISPR RNA (crRNA) at a limit of 102 copies/µL. Chemically synthesized and modified crRNAs greatly increase the CRISPR-LAMP signal, which advance the wide application. Combined with the previously developed RdRp CRISPR-LAMP assay, clinical results showed that Spike T478K and P681H can discriminate the mutant type form the wild type with 70% (49.66-85.50%, 95% confidence interval) and 78% (57.27-90.62%, 95% confidence interval) sensitivity, respectively, and 100% specificity (51.68-100%, 95% confidence interval), and the RdRp target can detect SARS-CoV-2 strains with 85% sensitivity (65.39-95.14%, 95% confidence interval) and 100% specificity (51.68-100%, 95% confidence interval). We believe that this automatic digital microfluid (DMF) system can advance the integrated CRISPR-LAMP technology with higher stability, sensitivity, and practicability, also for other CRISPR-associated diagnostic platforms.

Transcriptome and targeted metabolome analysis revealed the effects of combined red and blue light on the growth and secondary metabolism of Scutellaria baicalensis Georgi

Scutellaria baicalensis Georgi is a medicinal plant commonly used in China and other parts of East Asia. A high flavonoid content endows it with multiple beneficial biological activities that have anti-inflammatory, antibacterial, antiviral, and anti-COVID19 properties. Light-emitting diodes (LEDs) have been recognized as effective artificial lights to enhance plant growth and the accumulation of secondary metabolites for commercial plant production. However, little is known regarding the effects of LEDs on S. baicalensis. Here, we explored the effects of monochromatic blue light (B, 460 nm), monochromatic red light (R, 660 nm), white light (CK), and different combinations of R and B (R9B1, R7B3, R5B5, R3B7, and R1B9) on the growth of, and flavonoid accumulation in S. baicalensis. The results revealed that under R:B ratios of 9:1 or 7:3, the whole plant and roots of S. baicalensis seedlings had a higher biomass and flavonoid content. Targeted metabolomics analysis showed that 48 differentially expressed metabolites (DEMs) were verified between different groups, and the number of upregulated DEMs, particularly flavonoids, were higher in the R9B1 and R7B3 groups compared with the CK. Transcriptome data identified 1412 and 1508 differentially expressed genes (DEGs) in the R9B1 and R7B3 groups, respectively, in contrast to the CK. KEGG pathway analysis indicated that DEGs in both the R9B1 and R7B3 groups were primarily enriched in the phenylpropane biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, starch and sucrose metabolism, galactose metabolism, cartenoid biosynthesis, zeatin biosynthesis, and nitrogen metabolism pathways. The qRT-PCR results showed that SbPAL, SbCLL-7, SbCHI, SbFNS, and SbOMT encoding enzymes for the flavonoid biosynthesis pathway were significantly upregulated in S. baicalensis, which was consistent with the transcriptome data. Finally, based on correlation analysis between the main flavonoids in S. baicalensis and the genes encoding transcription factors and enzymes for the flavonoid metabolism pathway, a co-expression network map was developed, which provided a basis for the mining of light responsive genes related to flavonoids biosynthesis in S. baicalensis. This is the first report to articulate how the combination of red light and blue light influences the growth and secondary metabolism of S. baicalensis.

Systematic Analysis and Functional Characterization of R2R3-MYB Genes in Scutellaria baicalensis Georgi.

R2R3-MYB transcription factors participate in multiple critical biological processes, particularly as relates to the regulation of secondary metabolites. The dried root of Scutellaria baicalensis Georgi is a traditional Chinese medicine and possesses various bioactive attributes including anti-inflammation, anti-HIV, and anti-COVID-19 properties due to its flavonoids. In the current study, a total of 95 R2R3-MYB genes were identified in S. baicalensis and classified into 34 subgroups, as supported by similar exon-intron structures and conserved motifs. Among them, 93 R2R3-SbMYBs were mapped onto nine chromosomes. Collinear analysis revealed that segmental duplications were primarily responsible for driving the evolution and expansion of the R2R3-SbMYB gene family. Synteny analyses showed that the ortholog numbers of the R2R3-MYB genes between S. baicalensis and other dicotyledons had a higher proportion compared to that which is found from the monocotyledons. RNA-seq data indicated that the expression patterns of R2R3-SbMYBs in different tissues were different. Quantitative reverse transcriptase-PCR (qRT-PCR) analysis showed that 36 R2R3-SbMYBs from different subgroups exhibited specific expression profiles under various conditions, including hormone stimuli treatments (methyl jasmonate and abscisic acid) and abiotic stresses (drought and cold shock treatments). Further investigation revealed that SbMYB18/32/46/60/70/74 localized in the nucleus, and SbMYB18/32/60/70 possessed transcriptional activation activity, implying their potential roles in the regulatory mechanisms of various biological processes. This study provides a comprehensive understanding of the R2R3-SbMYBs gene family and lays the foundation for further investigation of their biological function.

Optimization, validation and analysis of a 2019-nCoV nucleic acid detection kit. (Special Issue: Spatio-temporal dynamics analysis, risk assessment and emergency management for COVID-19 epidemic.) [Chinese]

Objective: To optimize the sensitivity and specificity of a 2019-nCoV nucleic acid detection kit, so as to improve the positive detection rate and provide guidance for clinical use by comparison with different kits.

Quantification of SARS-CoV-2 RNA in wastewater treatment plants mirrors the pandemic trend in Hong Kong.

Wastewater-based epidemiology (WBE) for the SARS-CoV-2 virus in wastewater treatment plants (WWTPs) has emerged as a cost-effective and unbiased tool for population-level testing in the community. In the present study, we conducted a 6-month wastewater monitoring campaign from three WWTPs of different flow rates and catchment area characteristics, which serve 28 % (2.1 million people) of Hong Kong residents in total. Wastewater samples collected daily or every other day were concentrated using ultracentrifugation and the SARS-CoV-2 virus RNA in the supernatant was detected using the N1 and E primer sets. The results showed significant correlations between the virus concentration and the number of daily new cases in corresponding catchment areas of the three WWTPs when using 7-day moving average values (Kendall's tau-b value: 0.227-0.608, p < 0.001). SARS-CoV-2 virus concentration was normalized to a fecal indicator using PMMoV concentration and daily flow rates, but the normalization did not enhance the correlation. The key factors contributing to the correlation were also evaluated, including the sampling frequency, testing methods, and smoothing days. This study demonstrates the applicability of wastewater surveillance to monitor overall SARS-CoV-2 pandemic dynamics in a densely populated city like Hong Kong, and provides a large-scale longitudinal reference for the establishment of the long-term sentinel surveillance in WWTPs for WBE of pathogens which could be combined into a city-wide public health observatory.

Real-time allelic assays of SARS-CoV-2 variants to enhance sewage surveillance.

To effectively control the ongoing outbreaks of fast-spreading SARS-CoV-2 variants, there is an urgent need to add rapid variant detection and discrimination methods to the existing sewage surveillance systems established worldwide. We designed eight assays based on allele-specific RT-qPCR for real-time allelic discrimination of eight SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Omicron, Lambda, Mu, and Kappa) in sewage. In silico analysis of the designed assays for identifying SARS-CoV-2 variants using more than four million SARS-CoV-2 variant sequences yielded ∼100% specificity and >90% sensitivity. All assays could sensitively discriminate and quantify target variants at levels as low as 10 viral RNA copy/µL with minimal cross-reactivity to the corresponding nontarget genotypes, even for sewage samples containing mixtures of SARS-CoV-2 variants with differential abundances. Integration of this method into the routine sewage surveillance in Hong Kong successfully identified the Beta variant in a community sewage. Complete concordance was observed between the results of viral whole-genome sequencing and those of our novel assays in sewage samples that contained exclusively the Delta variant discharged by a clinically diagnosed COVID-19 patient living in a quarantine hotel. Our assays in this method also provided real-time discrimination of the newly emerging Omicron variant in sewage two days prior to clinical test results in another quarantine hotel in Hong Kong. These novel allelic discrimination assays offer a rapid, sensitive, and specific way for detecting multiple SARS-CoV-2 variants in sewage and can be directly integrated into the existing sewage surveillance systems.