Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins.

Malayan pangolin SARS-CoV-2-related coronavirus (SARSr-CoV-2) is closely related to SARS-CoV-2. However, little is known about its pathogenicity in pangolins. Using CT scans we show that SARSr-CoV-2 positive Malayan pangolins are characterized by bilateral ground-glass opacities in lungs in a similar manner to COVID-19 patients. Histological examination and blood gas tests are indicative of dyspnea. SARSr-CoV-2 infected multiple organs in pangolins, with the lungs the major target, and histological expression data revealed that ACE2 and TMPRSS2 were co-expressed with viral RNA. Transcriptome analysis indicated that virus-positive pangolins were likely to have inadequate interferon responses, with relative greater cytokine and chemokine activity in the lung and spleen. Notably, both viral RNA and viral proteins were detected in three pangolin fetuses, providing initial evidence for vertical virus transmission. In sum, our study outlines the biological framework of SARSr-CoV-2 in pangolins, revealing striking similarities to COVID-19 in humans.

Role of heat shock protein 90 as an antiviral target for swine enteric coronaviruses.

A variety of swine enteric coronaviruses (SECoVs) have emerged and are prevalent in pig populations, including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome (SADS)-CoV, a newly identified bat-origin CoV with zoonotic potential. Unfortunately, available traditional, inactivated and attenuated SECoV vaccines are of limited efficacy against the variants currently circulating in most pig populations. In this study, we evaluated the role of host factor heat shock protein 90 (Hsp90) as an antiviral target against SECoVs, exemplified by SADS-CoV. Pharmacological inhibition of Hsp90 diminished SADS-CoV replication significantly in porcine and human cell lines, and also decreased replication of SADS-CoV in a porcine intestinal enteroid model. Further mechanistic experiments revealed that both porcine and human isoforms of Hsp90 interact with the SADS-CoV nucleocapsid (N) protein, and inhibition of Hsp90 resulted in autophagic degradation of N protein. Moreover, we linked Hsp90 to virus-induced cellular pyroptosis, as SADS-CoV was found to trigger caspase-1/gasdermin-d-mediated pyroptotic cell death, which was mitigated by inhibition of Hsp90. Finally, we demonstrated that Hsp90 also associated with N proteins and was involved in propagation of PEDV, PDCoV and TGEV. This study thus extends our understanding of immune responses to SADS-CoV infection and offers a new potential therapeutic option against four SECoVs.

Psychological Health and Sleep Quality of Medical Graduates During the Second Wave of COVID-19 Pandemic in Post-epidemic Era.

Recently, a COVID-19 virus variant spread rapidly in Guangzhou, China, causing public panic. This study aimed to understand the psychological and sleep-related consequences of the secondary outbreak of the pandemic on medical students. In this cross-sectional survey-based study, participants anonymously completed structured questionnaires online from June 8-22, 2021. We collected participants' demographic and general information. Anxiety, depression, and sleep quality were measured using the Zung Self-Rating Anxiety Scale (SAS), Self-Rating Depression Scale (SDS), and Pittsburgh Sleep Quality Index (PSQI), respectively. Protective factors were assessed using the Coping Style Questionnaire (CSQ). Uni- and multivariate logistic regression analyses were performed examining factors associated with mental health and sleep quality problems. During the second wave of the pandemic in local outbreak areas in Guangzhou, China, more than one-third of medical students' mental health and sleep quality were affected. The prevalence of anxiety, depression, and poor sleep quality were 27.54%, 27.58%, and 18.19%, respectively. Students belonging to the Class of 2019, aged over 29 years, those with siblings, and those whose hometowns were in other provinces were more prone to the three health problems. Factors associated with an increased risk of mental health problems were vaccination status (adjusted odds ratio 1.603-1.839) and diet status (adjusted odds ratio 1.62-1.929). Positive coping styles served as protective factors (p < 0.05). We discovered that completed vaccination status, good diet, and positive coping styles were related to good mental health and sleep quality.

Diarrhoea outbreak caused by coinfections of Cryptosporidium parvum subtype IIdA20G1 and rotavirus in pre-weaned dairy calves.

Diarrhoea is one of the most important syndromes in neonatal calves. In industrialized nations with intensive animal farming, Cryptosporidium spp. and rotavirus are primary causes of calf diarrhoea, but the role of these and other enteric pathogens is not clear in China. In November and December 2018, a diarrhoea outbreak was identified in over 150 pre-weaned calves on a dairy farm in Heilongjiang Province, northeast China and approximately 60 calves died. To determine the cause of the outbreak, we analyzed 131 faecal samples collected from pre-weaned calves (0-2 months) during (n = 114) and after the outbreak (n = 17). Initially, 10 diarrheic samples during the outbreak and 10 non-diarrheic samples after the outbreak were screened for rotavirus, coronavirus, Escherichia coli K99 and Cryptosporidium parvum by using an enzymatic immunoassay (EIA). In addition, 81 other samples were tested specifically for rotavirus by EIA, and all 131 samples were analyzed for Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi by PCR. The initial EIA analysis identified C. parvum (8/10) and rotavirus (5/10) as the dominant pathogens in calves during the outbreak, while both pathogens were detected at lower frequency after the outbreak (2/10 and 1/10, respectively). Further PCR analyses indicated that the occurrence of C. parvum infections in calves was significantly higher during the outbreak (75.4%, 86/114) than after the outbreak (11.8%, 2/17; odds ratio [OR] = 23.0), and was significantly associated with the occurrence of watery diarrhoea (OR = 15.7) and high oocyst shedding intensity. All C. parvum isolates were identified as subtype IIdA20G1. Among other pathogens analyzed, the overall prevalence of rotavirus, G. duodenalis and E. bieneusi was 19.8% (20/101), 38.9% (51/131) and 42.0% (55/131) in calves, respectively, without significant differences during and after the outbreak. Among the three pathogens, only the rotavirus infection was associated with diarrhoea in calves. More importantly, coinfections of C. parvum and rotavirus were significantly associated with the occurrence of watery diarrhoea in calves and were seen only during the outbreak. Thus, C. parvum subtype IIdA20G1 and rotavirus appeared to be responsible for this diarrhoea outbreak. Control measures should be implemented to effectively prevent the concurrent transmission of these enteric pathogens in pre-weaned dairy calves in China.

Evaluation of the quality of COVID-19 prevention and control by a novel comprehensive evaluation model in a tertiary general hospital: a prospective observational study.

BACKGROUND: Prevention and control (P&C) of Corona Virus Disease 2019 (COVID-19) is still a critical task in most countries and regions. However, there are many single evaluation indexes to assess the quality of COVID-19 P&C. It is necessary to synthesize the single evaluation indexes reasonably to obtain the overall evaluation results. METHODS: This study was divided into three steps. Step 1: In February 2020, the improved Delphi method was used to establish the quality evaluation indexes system for COVID-19 P&C. Step 2: in March 2020, the CRITIC method was used to adjust the Order Relation Analysis (G1) method to obtain the subjective and objective (S&O) combination weights. The comprehensive evaluation value was obtained using the weighted Efficacy Coefficient (EC) method, weighted TOPSIS method, weighted rank-sum ratio (RSR) method, and weighted Grey Relationship Analysis (GRA) method. Finally, the linear normalization method was used to synthesize the evaluation values of different evaluation methods. Step 3: From April 2020 to May 2021, this evaluation method was used to monitor and assess COVID-19 P&C quality in critical departments prospectively. The results were reported to the departments monthly. RESULT: A quality evaluation indexes system for COVID-19 P&C was established. Kendall's consistency test shows that the four evaluation method had good consistency (χ2 = 43.429, P<0.001, Kendall's consistency coefficient = 0.835). The Spearman correlation test showed that the correlation between the combined evaluation results and the original method was statistically significant(P < 0.001). According to the Mann-Kendall test, from March 2020 to May 2021, the mean value of COVID-19 P&C quality in all critical departments showed an upward trend (P < 0.01). CONCLUSIONS: The combined comprehensive evaluation method based on the S&O combined weight was more scientific and comprehensive than the single weighting and evaluation methods. In addition, monitoring and feedback of COVID-19 P&C quality were helpful for the improvement of P&C quality.

Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2.

Since 2002, the world has witnessed major outbreaks of acute respiratory illness by three zoonotic coronaviruses (CoVs), which differ from each other in pathogenicity. Reasons for the lower pathogenicity of SARS-CoV-2 than the other two zoonotic coronaviruses, SARS-CoV and MERS-CoV, are not well understood. We herein compared the codon usage patterns of the three zoonotic CoVs causing severe acute respiratory syndromes and four human-specific CoVs (NL63, 229E, OC43, and HKU1) causing mild diseases. We found that the seven viruses have different codon usages, with SARS-CoV-2 having the lowest effective number of codons (ENC) among the zoonotic CoVs. Human codon adaptation index (CAI) analysis revealed that the CAI value of SARS-CoV-2 is the lowest among the zoonotic CoVs. The ENC and CAI values of SARS-CoV-2 were more similar to those of the less-pathogenic human-specific CoVs. To further investigate adaptive evolution within SARS-CoV-2, we examined codon usage patterns in 3573 genomes of SARS-CoV-2 collected over the initial 4 months of the pandemic. We showed that the ENC values and the CAI values of SARS-CoV-2 were decreasing over the period. The low ENC and CAI values could be responsible for the lower pathogenicity of SARS-CoV-2. While mutational pressure appears to shape codon adaptation in the overall genomes of SARS-CoV-2 and other zoonotic CoVs, the E gene of SARS-CoV-2, which has the highest codon usage bias, appears to be under strong natural selection. Data from the study contribute to our understanding of the pathogenicity and evolution of SARS-CoV-2 in humans.

Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins.

The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins-the most-trafficked mammal in the illegal wildlife trade-could represent a future threat to public health if wildlife trade is not effectively controlled.