Isolation of a Novel Bat Rhabdovirus with Evidence of Human Exposure in China.

Bats are well-recognized reservoirs of zoonotic viruses. Several spillover events from bats to humans have been reported, causing severe epidemic or endemic diseases including severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), SARS-CoV, Middle East respiratory syndrome-CoV (MERS-CoV), henipaviruses, and filoviruses. In this study, a novel rhabdovirus species, provisionally named Rhinolophus rhabdovirus DPuer (DPRV), was identified from the horseshoe bat (Rhinolophus affinis) in Yunnan province, China, using next-generation sequencing. DPRV shedding in the spleen, liver, lung, and intestinal contents of wild bats with high viral loads was detected by real-time quantitative PCR, indicating that DPRV has tropism for multiple host tissues. Furthermore, DPRV can replicate in vitro in multiple mammalian cell lines, including BHK-21, A549, and MA104 cells, with the highest efficiency in hamster kidney cell line BHK-21, suggesting infectivity of DPRV in these cell line-derived hosts. Ultrastructure analysis revealed a characteristic bullet-shaped morphology and tightly clustered distribution of DPRV particles in the intracellular space. DPRV replicated efficiently in suckling mouse brains and caused death of suckling mice; death rates increased with passaging of DPRV in suckling mice. Moreover, 421 serum samples were collected from individuals who lived near the bat collection site and had fever symptoms within 1 year. DPRV-specific antibodies were detected in 20 (4.75%) human serum samples by indirect immunofluorescence assay. Furthermore, 10 (2.38%) serum samples were DPRV positive according to plaque reduction neutralization assay, which revealed potential transmission of DPRV from bats to humans and highlighted the potential public health risk. Potential vector association with DPRV was not found with negative viral RNA in bloodsucking arthropods. IMPORTANCE We identified a novel rhabdovirus from the horseshoe bat (Rhinolophus thomasi) in China with probable infectivity in humans. DPRV was isolated in vitro from several mammalian cell lines, indicating wide host tropism, excluding bats, of DPRV. DPRV replicated in the brains of suckling mice, and the death rate of suckling mice increased with passaging of DPRV in vivo. Serological tests indicated the possible infectivity of DPRV in humans and the potential transmission to humans. The present findings provide preliminary evidence for the potential risk of DPRV to public health. Additional studies with active surveillance are needed to address interspecies transmission and determine the pathogenicity of DPRV in humans.

Research Trends in Lung Organoids: Bibliometric Analysis and Visualization (preprint)

Background Lung organoids have emerged as a promising tool for studying lung development, function, and disease pathology. The present study aimed to analyze the current status and development trends of lung organoid research over the past years, present visual representations, and provide references for future research directions using bibliometric analysis.Methods Information on articles on lung organoids extracted from the Web of Science Core Collection, such as year of publication, journal, country, institution, author, and keywords, was analyzed. R, VOSviewer, and SCImago Graphica were used to visualize publication trends, co-authorship analysis, co-occurrence analysis, and hotspot evolution.Results The number of global publications has increased from 1 in 2011 to 512 in 2022. The cell produced the highest number of citations (2,069 citations). The United States (6,694 citations and 177 publications), University Medical Center Utrecht (2,060 citations and 9 publications), and Clevers H (2,570 citations and 15 publications) were the most influential countries, institutions, and authors, respectively. Co-occurrence cluster analysis of the top 54 keywords formed four clusters: (1) pulmonary fibrosis (PF), (2) lung cancer, (3) cystic fibrosis (CF), (4) coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).Conclusion Organoid technology undoubtedly played an important role in the study of COVID-19, but with the passing of the COVID-19 epidemic, the research focus may return to refractory lung diseases such as PF, CF, and lung cancer. Standardized culture, living biobanks, and multimodal model systems for lung disease may be the future research directions in the field of lung organoids.

Transformer for one stop interpretable cell type annotation.

Consistent annotation transfer from reference dataset to query dataset is fundamental to the development and reproducibility of single-cell research. Compared with traditional annotation methods, deep learning based methods are faster and more automated. A series of useful single cell analysis tools based on autoencoder architecture have been developed but these struggle to strike a balance between depth and interpretability. Here, we present TOSICA, a multi-head self-attention deep learning model based on Transformer that enables interpretable cell type annotation using biologically understandable entities, such as pathways or regulons. We show that TOSICA achieves fast and accurate one-stop annotation and batch-insensitive integration while providing biologically interpretable insights for understanding cellular behavior during development and disease progressions. We demonstrate TOSICA's advantages by applying it to scRNA-seq data of tumor-infiltrating immune cells, and CD14+ monocytes in COVID-19 to reveal rare cell types, heterogeneity and dynamic trajectories associated with disease progression and severity.

A digitized catalog of COVID-19 epidemiology data

COVID-19 is now rapidly spreading worldwide. While the majority of COVID-19 patients show only mild or moderate symptoms, some could deteriorate quickly and may succumb to a sudden death. It is therefore important to identify who will be more likely to develop severe outcomes and be treated with particular or preventive care. Here in this literature survey, we collected epidemiologic and clinical data from 36 articles on 51,270 patients with different severity of COVID-19, aiming to characterize the population that are prone to severe condition and bad outcomes. These data reveal that old males and those with high BMI or underlying diseases, especially cardiovascular disease, hypertension and diabetes, are overrepresented among severe cases. High leukocyte and lymphopenia are common features in severe and critical patients. Upon deterioration of the disease, both CD4 and CD8 T cells are decreased, while almost all serum cytokines, especially pro-inflammatory cytokines, increased.

ACE2 in the Gut: The Center of the 2019-nCoV Infected Pathology.

The 2019-nCoV is a rapidly contagious pneumonia caused by the recently discovered coronavirus. Although generally the most noticeable symptoms are concentrated in the lungs, the disorders in the gastrointestinal tract are of great importance in the diagnosis of 2019-nCoV. The angiotensin-converting enzyme 2 (ACE2), an important regulator of many physiological functions, including blood pressure and nutrients absorption, is recently identified as a vital entry for 2019-nCoV to enter host cells. In this review, we summarize its functions both physiologically and pathologically. We also elaborate its conflicting roles from the clews of contemporary researches, which may provide significant indications for pharmacological investigations and clinical uses.

The feasibility of yupingfengsan to prevent new coronavirus pneumonia

The new type of coronavirus pneumonia (new coronary pneumonia for short), due to its strong infectivity and rapid spread, poses a major threat to public health and greatly increases the burden on society. Since there is no specific medicine for new coronary pneumonia, prevention and stopping the spread of the epidemic are the focus of epidemic prevention work. The new crown pneumonia belongs to the category of "epidemic" and "plague" in Chinese medicine. Epidemics have been pandemic in ancient China. Either "Huangdi Neijing", "Treatise on Febrile Diseases", or in the works of the Febrile Disease School in the Ming and Qing Dynasties, we can see the discussion of "disease". For thousands of years, Chinese medicine has accumulated accumulated efforts in preventing the spread and prevalence of the epidemic in the process of constantly fighting against the epidemic.

Follow-up testing of viral nucleic acids in patients with COVID-19 in Dazu district, Chongqing, China

To investigate the recurrence rate of coronavirus disease 2019(COVID-19) after discharge and type of SARS-CoV-Z nucleic acid-positive samples from patients with recurrence of SARS-CoV-Z in Dazu District, Chongqing, China, all patients were kept in isolation for 14 days, then quarantined at home for 4 weeks after discharge, during which time nasopharyngeal swabs, oropharyngeal swabs, feces, saliva, and urine were collected to test for SARS-CoV-Z nucleic acids by RT-PCR, and symptoms and signs were documented. Results showed that there were no symptoms or signs during isolation for any patient. However, specimens from three patients were confirmed positive for SARS-CoV-Z nucleic acids 3 to 14 days after discharge. SARS- CoV-Z nucleic acids were detected in saliva samples from two patients with recurrence of SARS-CoV-Z. The present study suggested that there is a relatively high incidence of positive tests for SARS-CoV-Z nucleic acids in patients after discharge. This is the first time that SARS-CoV-Z nucleic acids were detected in saliva samples. Whether the virus is infectious in these patients requires further study.

Recombinant SARS-CoV-2 RBD with a built in T helper epitope induces strong neutralization antibody response.

Without approved vaccines and specific treatments, COVID-19 is spreading around the world with above 26 million cases and approximately 864 thousand deaths until now. An efficacious and affordable vaccine is urgently needed. The Val308 - Gly548 of spike protein of SARS-CoV-2 linked with Gln830 - Glu843 of Tetanus toxoid (TT peptide) (designated as S1-4) and without TT peptide (designated as S1-5) were expressed and renatured. The antigenicity and immunogenicity of S1-4 were evaluated by Western Blotting (WB) in vitro and immune responses in mice, respectively. The protective efficiency was measured preliminarily by microneutralization assay (MN50). The soluble S1-4 and S1-5 protein was prepared to high homogeneity and purity. Adjuvanted with Alum, S1-4 protein stimulated a strong antibody response in immunized mice and caused a major Th2-type cellular immunity supplemented with Th1-type immunity. Furthermore, the immunized sera could protect the Vero E6 cells from SARS-CoV-2 infection with neutralizing antibody titer 256. Recombinant SARS-CoV-2 RBD with a built in T helper epitope could stimulate both strong humoral immunity supplemented with cellular immunity in mice, demonstrating that it could be a promising subunit vaccine candidate.

A human circulating immune cell landscape in aging and COVID-19.

Age-associated changes in immune cells have been linked to an increased risk for infection. However, a global and detailed characterization of the changes that human circulating immune cells undergo with age is lacking. Here, we combined scRNA-seq, mass cytometry and scATAC-seq to compare immune cell types in peripheral blood collected from young and old subjects and patients with COVID-19. We found that the immune cell landscape was reprogrammed with age and was characterized by T cell polarization from naive and memory cells to effector, cytotoxic, exhausted and regulatory cells, along with increased late natural killer cells, age-associated B cells, inflammatory monocytes and age-associated dendritic cells. In addition, the expression of genes, which were implicated in coronavirus susceptibility, was upregulated in a cell subtype-specific manner with age. Notably, COVID-19 promoted age-induced immune cell polarization and gene expression related to inflammation and cellular senescence. Therefore, these findings suggest that a dysregulated immune system and increased gene expression associated with SARS-CoV-2 susceptibility may at least partially account for COVID-19 vulnerability in the elderly.

Individual variation of the SARS-CoV-2 receptor ACE2 gene expression and regulation.

The COVID-19 coronavirus is now spreading worldwide. Its pathogen, SARS-CoV-2, has been shown to use angiotensin-converting enzyme 2 (ACE2) as its host cell receptor, same as the severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. Epidemiology studies found males although only slightly more likely to be infected than females account for the majority of the severely ill and fatality, which also bias for people older than 60 years or with metabolic and cardiovascular diseases. Here by analyzing GTEx and other public data in 30 tissues across thousands of individuals, we found a significantly higher level in Asian females, an age-dependent decrease in all ethnic groups, and a highly significant decrease in type II diabetic patients of ACE2 expression. Consistently, the most significant expression quantitative loci (eQTLs) contributing to high ACE2 expression are close to 100% in East Asians, >30% higher than other ethnic groups. A shockingly common enrichment of viral infection pathways was found among ACE2 anti-expressed genes, and multiple binding sites of virus infection related transcription factors and sex hormone receptors locate at ACE2 regulatory regions. Human and mice data analysis further revealed ACE2 expression is reduced in T2D patients and with inflammatory cytokine treatment and upregulated by estrogen and androgen (both decrease with age). Our findings revealed a negative correlation between ACE2 expression and COVID-19 fatality at both population and molecular levels. These results will be instrumental when designing potential prevention and treatment strategies for ACE2 binding coronaviruses in general.