Oral health behaviors for young low-income urban children during the COVID-19 pandemic: a mixed methods analysis (preprint)

This research assessed oral health behaviors changes in urban families with young children during the stay-at-home period of the COVID-19 pandemic. Survey data on oral health behaviors were collected in homes at three points over one year before COVID-19, and then via phone during COVID-19. Multivariate logistic regression was used to model tooth brushing frequency. A subset of parents completed in-depth interviews via video/phone that expanded on oral health and COVID-19. Key informant interviews via video/phone were also conducted with leadership from 20 clinics and social service agencies. Interview data were transcribed and coded, and themes were extracted. COVID-19 data collection went from Nov 2020 – August 2021. Of the 387 parents invited, 254 completed surveys in English or Spanish (65.6%) during COVID-19. Fifteen key informant (25 participants) and 21 parent interviews were conducted. The mean child age was approximately 4.3 years. Children identified as mainly Hispanic (57%) and Black race (38%). Parents reported increased child tooth brushing frequency during the pandemic. Parent interviews highlighted significant changes in family routines that impacted oral health behaviors and eating patterns, suggesting less optimal brushing and nutrition. This was linked to changed home routines and social presentability. Key informants described major disruptions in their oral health services and significant family fear and stress. In conclusion, the stay-at-home period of the COVID-19 pandemic was a time of extreme routine change and stress for families. Oral health interventions that target family routines and social presentability are important for families during times of extreme crisis.

Longitudinal wastewater surveillance addressed public health priorities during the transition from "dynamic COVID-zero" to "opening up" in China: a population-based study (preprint)

Background Wastewater surveillance provides real-time, cost-effective monitoring of SARS-CoV-2 transmission. We developed the first city-level wastewater warning system in mainland China, located in Shenzhen. Our study aimed to reveal cryptic transmissions under the "dynamic COVID-zero" policy and characterize the dynamics of the infected population and variant prevalence, and then guide the allocation of medical resources during the transition to "opening up" in China. Methods In this population-based study, a total of 1,204 COVID-19 cases were enrolled to evaluate the contribution of Omicron variant-specific faecal shedding rates in wastewater. After that, wastewater samples from up to 334 sites distributed in communities and port areas in two districts of Shenzhen covering 1.74 million people were tested daily to evaluate the sensitivity and specificity of this approach and were validated against daily SARS-CoV-2 screening. After the public health policy was switched to "opening up" in December 7, 2022, we conducted wastewater surveillance at wastewater treatment plants and pump stations covering 3.55 million people to estimate infected populations using model prediction and detect the relative abundance of SARS-CoV-2 lineages using wastewater sequencing. Findings In total, 82.4% of SARS-CoV-2 Omicron cases tested positive for faecal viral RNA within the first four days after the diagnosis, which was far more than the proportion of the ancestral variant. A total of 27,759 wastewater samples were detected from July 26 to November 30 in 2022, showing a sensitivity of 73.8% and a specificity of 99.8%. We further found that wastewater surveillance played roles in providing early warnings and revealing cryptic transmissions in two communities. Based on the above results, we employed a prediction model to monitor the daily number of infected individuals in Shenzhen during the transition to "opening up" in China, with over 80% of the population infected in both Futian District and Nanshan District. Notably, the prediction of the daily number of hospital admission was consistent with the actual number. Further sequencing revealed that the Omicron subvariant BA.5.2.48 accounted for the most abundant SARS-CoV-2 RNA in wastewater, and BF.7.14 and BA.5.2.49 ranked second and third, respectively, which was consistent with the clinical sequencing. Interpretation This study provides a scalable solution for wastewater surveillance of SARS-CoV-2 to provide real-time monitoring of the new variants, infected populations and facilitate the precise prediction of hospital admission. This novel framework could be a One Health system for the surveillance of other infectious and emerging pathogens with faecal shedding and antibiotic resistance genes in the future. Funding Sanming Project of Medicine in Shenzhen, Shenzhen Key Medical Discipline Construction Fund.

Constructing a diversified online neurology teaching model under the COVID-19

Purpose To construct a diversified and comprehensive network teaching model to provide highly qualified medical teaching in neurology under COVID-19 pandemic. Materials and methods Published studies on medical education were systematically reviewed and summarized. Based on previous studies and our experience, we constructed a novel online neurology teaching model and applied it to real scene. Students taking traditional in class lessons and online lessons were asked to finish the test, respectively, to compare the efficiency of learning. Questionnaires were designed and assigned to get the feedback from students. Results The average test score of students who take online class (84.27 ± 4.64) was significantly higher than those who take in class lessons (82.08 ± 6.17) (P < 0.01). According to the feedbacks from students, online classes were more attractive to students than the conventional one. Conclusion Traditional single-mode teaching can no longer meet the needs of current medical education, especially under the rampant epidemic. This novel teaching mode, which orchestrates high-tech tools, diverse teaching methods and traditional teaching concepts, provides the solution to the challenge faced by traditional medical education. We believe that this novel online teaching mode will boost neurology education and inspire educators in other fields during this tough period.

Breakthrough infection with Omicron subvariant BF.7 induces broadly neutralizing antibodies to SARS-CoV-2 variants including XBB lineage (preprint)

Since China eased its COVID-19 response strategies in late 2022, we have been witnessing a rapid and wide spread of SARS-CoV-2 infection across the major cities, including capital Beijing, where Omicron subvariant BF.7 has been dominating the infection. Here, we show that such expansion is unlikely due to a higher binding affinity of BF.7 to human receptor angiotensin-converting enzyme 2 (ACE2) as the similar binding activities were found for other Omicron subvariants tested such as BA.1, BA.5.2, BQ.1, BQ.1.1, XBB, and XBB.1. Additionally, through study of antibody response among six different clinical cohorts, we found that primary infection with BF.7 among the unvaccinated individuals only elicited type-specific neutralizing antibodies to the infecting virus and its close related strains. By a distinct contrast, breakthrough infection with BF.7 among the vaccinated individuals, particularly those severe cases, induced strong and broadly neutralizing antibodies to a diverse panel of SARS-CoV-2 variants and Omicron subvariants including the XBB lineage. A deeper understanding of how these broadly neutralizing antibodies were generated or boosted by BF.7 breakthrough infection will hold the key for augmenting antibody immunity against diverse SARS-CoV-2 variants.

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.

Exploring the Regulatory Function of the N‐terminal Domain of SARS‐CoV‐2 Spike Protein through Molecular Dynamics Simulation

SARS‐CoV‐2 is what has caused the COVID‐19 pandemic. Early viral infection is mediated by the SARS‐CoV‐2 homo‐trimeric Spike (S) protein with its receptor binding domains (RBDs) in the receptor‐accessible state. Molecular dynamics simulation on the S protein with a focus on the function of its N‐terminal domains (NTDs) is performed. The study reveals that the NTD acts as a “wedge” and plays a crucial regulatory role in the conformational changes of the S protein. The complete RBD structural transition is allowed only when the neighboring NTD that typically prohibits the RBD's movements as a wedge detaches and swings away. Based on this NTD “wedge” model, it is proposed that the NTD–RBD interface should be a potential drug target. The Spike protein of SARS‐CoV‐2 plays a key role in the infection process. The N‐terminal domain (NTD) of the Spike protein plays a regulatory function by the “wedge” model: it typically wedges in to prohibit receptor binding domain's (RBD's) movements and occasionally moves out to allow RBD to tilt downward. Potential drugs are virtually screened for the NTD‐RBD interface.

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation (Adv. Theory Simul. 10/2021)

N-terminal Domain of SARS-CoV-2 Spike Protein In article number 2100152, Yao Li, Tong Wang, Haipeng Gong, and co-workers propose the ?wedge? model to demonstrate the regulatory function of the N-terminal domain (NTD) of SARS-CoV-2 Spike protein. The NTD typically wedges in to prohibit receptor binding domain's (RBD's) movements and it occasionally moves out to allow RBD to tilt downward.

Switching to electric vehicles can lead to significant reductions of PM2.5 and NO2 across China

Summary Transportation contributes to around one-fifth of global greenhouse gas emissions, while also causing severe air pollution. The conversion to electric vehicles (EVs) represents a major path to decarbonize the transport sector, with potentially significant co-benefits for human health. However, the scale of such co-benefits largely remains an empirical question and lacks observational evidence. The full lockdown in China during the coronavirus disease 2019 (COVID-19) pandemic provides an unprecedented real-world experiment to evaluate emission reduction potentials of a large-scale transition to EVs. Here, we utilize ground and satellite observations of air quality during the full lockdown to constrain predictions of a comprehensive chemical transport model and find that the substantial traffic reductions are near-linearly linked to reductions of PM2.5 (particles with an aerodynamic diameter ≤2.5 μm) and NO2. A further extrapolation of a full conversion to EVs shows a significant reduction of PM2.5 (30%–70%) and NO2 (30%–80%) in most of China. Our findings provide fact-based evidence of potential environmental benefits generated by fully switching to EVs.

Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions (preprint)

SARS-CoV-2 has emerged as a major threat to global public health, resulting in global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 virus in cells using high throughput structure probing on Illumina and Nanopore platforms. We identified twelve potentially functional structural elements within the SARS-CoV-2 genome, observed that identical sequences can fold into divergent structures on different subgenomic RNAs, and that WT and Δ382 virus genomes can fold differently. Proximity ligation sequencing experiments identified hundreds of intramolecular and intermolecular pair-wise interactions within the virus genome and between virus and host RNAs. SARS-CoV-2 binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2’-O-methylated. 2’-O-methylation sites in the virus genome are enriched in the untranslated regions and are associated with increased pair-wise interactions. SARS-CoV-2 infection results in a global decrease of 2’-O-methylation sites on host mRNAs, suggesting that binding to snoRNAs could be a pro-viral mechanism to sequester methylation machinery from host RNAs towards the virus genome. Collectively, these studies deepen our understanding of the molecular basis of SARS-CoV-2 pathogenicity, cellular factors important during infection and provide a platform for targeted therapy.

Spike mutations in SARS-CoV-2 variants confer resistance to antibody neutralization (preprint)

New SARS-CoV-2 variants continue to emerge from the current global pandemic, some of which can replicate faster and with greater transmissibility and pathogenicity. In particular, UK501Y.V1 identified in UK, SA501Y.V2 in South Africa, and BR501Y.V3 in Brazil are raising serious concerns as they spread quickly and contain spike protein mutations that may facilitate escape from current antibody therapies and vaccine protection. Here, we constructed a panel of 28 SARS CoV 2 pseudoviruses bearing single or combined mutations found in the spike protein of these three variants, as well as additional nine mutations that within or close by the major antigenic sites in the spike protein identified in the GISAID database. These pseudoviruses were tested against a panel of monoclonal antibodies (mAbs), including some approved for emergency use to treat SARS CoV 2 infection, and convalescent patient plasma collected early in the pandemic. SA501Y.V2 pseudovirus was the most resistant, in magnitude and breadth, against mAbs and convalescent plasma, followed by BR501Y.V3, and then UK501Y.V1. This resistance hierarchy corresponds with Y144del and 242-244del mutations in the N-terminal domain as well as K417N/T, E484K and N501Y mutations in the receptor binding domain (RBD). Crystal structural analysis of RBD carrying triple K417N E484K N501Y mutations found in SA501Y.V2 bound with mAb P2C-1F11 revealed a molecular basis for antibody neutralization and escape. SA501Y.V2 and BR501Y.V3 also acquired substantial ability to use mouse and mink ACE2 for entry. Taken together, our results clearly demonstrate major antigenic shifts and potentially broadening the host range of SA501Y.V2 and BR501Y.V3, which pose serious challenges to our current antibody therapies and vaccine protection.

Towards Unbiased COVID-19 Lesion Localisation and Segmentation via Weakly Supervised Learning (preprint)

Despite tremendous efforts, it is very challenging to generate a robust model to assist in the accurate quantification assessment of COVID-19 on chest CT images. Due to the nature of blurred boundaries, the supervised segmentation methods usually suffer from annotation biases. To support unbiased lesion localisation and to minimise the labeling costs, we propose a data-driven framework supervised by only image-level labels. The framework can explicitly separate potential lesions from original images, with the help of a generative adversarial network and a lesion-specific decoder. Experiments on two COVID-19 datasets demonstrate the effectiveness of the proposed framework and its superior performance to several existing methods.

Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules (preprint)

Summary: Recently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on the ACE2/dACE2 locus. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating between ACE2 and dACE2 revealed 300- and 600-fold upregulation of dACE2 by IFN and IFN{beta}, respectively, while full length ACE2 expression was almost unchanged. JAK inhibitor ruxolitinib ablated STAT1 and dACE2 expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule cells.

Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions (preprint)

SARS-CoV-2 has emerged as a major threat to global public health, resulting in global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype (WT) and a mutant ({Delta}382) SARS-CoV-2 virus in cells using high throughput structure probing on Illumina and Nanopore platforms. We identified twelve potentially functional structural elements within the SARS-CoV-2 genome, observed that identical sequences can fold into divergent structures on different subgenomic RNAs, and that WT and {Delta}382 virus genomes can fold differently. Proximity ligation sequencing experiments identified hundreds of intramolecular and intermolecular pair-wise interactions within the virus genome and between virus and host RNAs. SARS-CoV-2 binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2'-O-methylated. 2'-O-methylation sites in the virus genome are enriched in the untranslated regions and are associated with increased pair-wise interactions. SARS-CoV-2 infection results in a global decrease of 2'-O-methylation sites on host mRNAs, suggesting that binding to snoRNAs could be a pro-viral mechanism to sequester methylation machinery from host RNAs towards the virus genome. Collectively, these studies deepen our understanding of the molecular basis of SARS-CoV-2 pathogenicity, cellular factors important during infection and provide a platform for targeted therapy.

Autopsy and Statistical Evidence of Disturbed Hemostasis Progress in COVID-19: Medical Records from 407 Patients (preprint)

Background: The progression of coagulation in COVID-19 patients with confirmed discharge status and the combination of autopsy with complete hemostasis parameters have not been well studied. Objective: To clarify the thrombotic phenomena and hemostasis state in COVID-19 patients based on epidemiological statistics combining autopsy and statistical analysis. Methods: : Using autopsy results from 9 patients with COVID-19 pneumonia and the medical records of 407 patients, including 39 deceased patients whose discharge status was certain, time-sequential changes in 11 relevant indices within mild, severe and critical infection throughout hospitalization according to the Chinese National Health Commission (NHC) guidelines were evaluated. Statistical tools were applied to calculate the importance of 11 indices and the correlation between those indices and the severity of COVID-19. Results: : At the beginning of hospitalization, platelet (PLT) counts were significantly reduced in critically ill patients compared with severely or mildly ill patients. Blood glucose (GLU), prothrombin time (PT), activated partial thromboplastin time (APTT), and D-dimer levels in critical patients were increased compared with mild and severe patients during the entire admission period. The International Society on Thrombosis and Haemostasis (ISTH) disseminated intravascular coagulation (DIC) score was also high in critical patients. In the relatively late stage of nonsurvivors, the temporal changes in PLT count, PT, and D-dimer levels were significantly different from those in survivors. A random forest model indicated that the most important feature was PT followed by D-dimer, indicating their positive associations with disease severity. Autopsy of deceased patients fulfilling diagnostic criteria for DIC revealed microthromboses in multiple organs. Conclusions: Combining autopsy data, time-sequential changes and statistical methods to explore hemostasis-relevant indices among the different severities of the disease helps guide therapy and detect prognosis in COVID-19 infection.

A repurposed, blood gene signature is associated with poor outcomes in SARS-CoV-2 (preprint)

Poor outcomes after SARS-CoV-2 infection are difficult to predict. Survivors may develop pulmonary fibrosis. We previously identified a 52-gene signature in peripheral blood, predictive of mortality in Idiopathic Pulmonary Fibrosis. In this study, we analyzed this signature in SARS-CoV-2 infected individuals and identified genomic risk profiles with significant differences in outcomes. Analysis of single cell expression data shows that monocytes, red blood cells, neutrophils and dendritic cells are the cellular source of the high risk gene signature.

Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients (preprint)

Dysfunctional immune response in the COVID-19 patients is a recurrent theme impacting symptoms and mortality, yet the detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 205 COVID-19 patients and controls to create a comprehensive immune landscape. Lymphopenia and active T and B cell responses were found to coexist and associated with age, sex and their interactions with COVID-19. Diverse epithelial and immune cell types were observed to be virus-positive and showed dramatic transcriptomic changes. Elevation of ANXA1 and S100A9 in virus-positive squamous epithelial cells may enable the initiation of neutrophil and macrophage responses via the ANXA1-FPR1 and S100A8/9-TLR4 axes. Systemic up-regulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis and designing effective therapeutic strategies for COVID-19.