Genetic features of bovine viral diarrhea virus subgenotype 1c in newborn calves at nucleotide and synonymous codon usages

Bovine viral diarrhea virus (BVDV), serving as an important pathogen for newborn calves, poses threat to reproductive and economic losses in the cattle industry. To survey the infection rate and genetic diversity of BVDV in newborn calves in northern China, a total of 676 sera samples of newborn calves were collected from four provinces between 2021 and 2022. All sera samples were individually detected for BVDV infection by RT-PCR and ELISA. Our results showed that the overall serological rate was 9.76% (66/676) and the average positive rate of BVDV RNA was 8.14% (55/676) in the newborn calves. Eight BVDV strains were successfully isolated from RT-PCR positive sera samples, and four isolates displayed the cytopathic effect (CPE). Based on phylogenetic tree at the genome level, the eight strains were classified into subgenotype 1c. Moreover, the BVDV isolates had a close genetic relationship with the GSTZ strain at either nucleotide or codon usage level. Interestingly, in comparison of synonymous codon usage patterns between the BVDV isolates with CPE and ones without CPE, there were four synonymous codons (UCG, CCC, GCA, and AAC) which displayed the significant differences (p < 0.05) at codon usage pattern, suggesting that synonymous codon usage bias might play a role in BVDV-1c biotypes. In addition, the usage of synonymous codons containing CpG dinucleotides was suppressed by the BVDV-1c isolates, reflecting one of strategies of immune evasion of BVDV to its host. Taken together, our study provided data for monitoring and vaccination strategies of BVDV for newborn calves in northern China.

Yak Gut Microbiota: A Systematic Review and Meta-Analysis

The yak (Bos grunniens) is closely related to common cows (Bos taurus), but is clearly a distinct species. Yaks are of substantial importance to food and leather production in certain high-altitude regions of Asia. The animal is increasing elsewhere as well, mainly because of the perceived health benefits of its milk. Like all ruminants, the animal harbors a complex community of microbial cells in its gut, crucial for its physiology. Despite yaks being important domestic animals, the composition of its gut microbiota and how the composition is guided by its specific high-altitude environment remains largely uncategorized. Hence, online databases (Embase, Medline ALL, Web of Science Core Collection, Cochrane Central Register of Controlled Trials, and Google Scholar) were searched for articles on yak intestinal microbiota. The pooled taxonomic abundance was compared between regions, sexes, different age groups, and feeding patterns. The gut microbiota distribution across different yak intestinal segments was established through pooled average taxonomic abundance. A total of 34 studies met the inclusion criteria and yielded information on 982 unique yak gut microbiota samples. An analysis of overall pooled microbiota revealed a segmented microbial community composition of the yak gut. Yak rumen microbiota was significantly influenced by difference in region, sex, and feeding patterns, the latter factor being dominant in this respect. Yak microbiome is shaped by the feeding strategy and provides an obvious avenue for improving health and productivity of the animal. More generally, the current segmental description of physiological gut microbiome provides insight into how the microbiology of this animal has adapted itself to help comping yaks with its high-altitude habitat.

[A case report of acute methyl acetate poisoning in cloth processing workshop]

This article analyzed the clinical data of a patient with occupational chemical poisoning in a fabric processing workshop in August 2020, and carried out occupational hygiene investigation and testing. The patient went to the doctor because of painless progressive vision loss in both eyes, and was clinically diagnosed with methanol poisoning optic neuropathy in both eyes. The glue, solvent, washing machine water, and curing agent used in the workshop were used for qualitative analysis of volatile organic components, and methyl acetate was all detected. Esters, the relative percentages were 42.56%, 66.67%, 46.43%, and 41.63%, respectively. Therefore, it was judged that the patient was occupational acute methyl acetate poisoning, the enterprise should strengthen the awareness of safe production and enhance the occupational hygiene knowledge and self-protection awareness of workers.

Investigating Ramadan Like Fasting Effects on the Gut Microbiome in BALB/c Mice

Recently we reported that in healthy volunteer Ramadan-associated intermittent fasting (RAIF) remodels the gut microbiome and resulted in an increase in small chain fatty acid producing bacteria concomitant with improved metabolic parameters. As interpretation of these results is hampered by the possible psychological effects associated with the study, we now aim to investigate RAIF in experimental animals. To this end, 6-week male BALB/c mice were subjected to RAIF (30 days of a 16-h daily fasting; n = 8) or provided with feed ad libitum (n = 6). Fecal samples were collected before and the end of fasting and bacterial 16S rRNA sequencing was performed. We found that RAIF remodeled the composition of gut microbiota in BALB/c mice (p < 0.01) and especially provoked upregulation of butyrate acid-producing Lachnospireceae and Ruminococcaceae (p < 0.01), resembling the effects seen in human volunteers. Hence we conclude that the effects of RAIF on gut microbiome relate to the timing of food intake and are not likely related to psychological factors possibly at play during Ramadan.

[Clinical value of routine contrast esophagram in the diagnosis of anastomotic leakage for three-incision esophagectomy with cervical anastomosis]

Objective: To examine the clinical value of routine contrast esophagram (RCE) for the diagnosis of anastomotic leakage (AL) after three-incision esophagectomy with cervical anastomosis. Methods: Clinical data of 1 022 patients with esophageal cancer who underwent McKeown three-incision esophagectomy with cervical anastomosis from January 2015 to December 2019 at Department of Minimally Invasive Esophageal Surgery, Tianjin Medical University Cancer Hospital and Institute were analyzed retrospectively. There were 876 males and 146 females, aging(M(IQR)) 48(16) years (range: 36 to 84 years). There were 253 patients (24.8%) with neoadjuvant therapy, and 817 patients (79.9%) with minimally invasive esophagectomy. According to the diagnosis and treatment habits of the attending surgeons, 333 patients were included in the RCE group, and RCE was performed on the 7^th day postoperative, while 689 patients were included in the non-RCE group, and RCE was performed when the patients had suspicious symptoms. Taking clinical symptoms, RCE, CT, endoscopy and other methods as reference to the diagnosis of AL, the sensitivity and specificity were used to analyze and evaluate the efficacy of RCE for the diagnosis of AL. The data were compared by U test or χ² test between groups. Results: The incidence rate of AL after three-incision esophagectomy was 7.34% (75/1 022), including 30 cases in the RCE group and 45 cases in the non-RCE group (9.0%(30/333) vs. 6.5%(45/689), χ²=2.027, P=0.155). The diagnostic time of AL was 9(5) days postoperative (range: 4 to 30 days). Among them, 23 cases showed cervical leakages, 50 cases showed intro-thoracic leakages, and 2 cases both cervical and intro-thoracic leakages. The diagnostic time of patients with intro-thoracic leakages was longer than that of cervical leakages (10(4) days vs. 6(3) days, Z=-2.517, P=0.012). Among the 333 patients in the RCE group, 16 cases of RCE indicated leakages including 11 cases of true positive and 5 cases determined to be false positive, while 317 cases indicated no abnormalities including 19 cases developed leakages. The sensitivity and specificity of RCE to detect AL were 36.7%(11/30) and 98.3%(298/333), respectively. The Youden-index was 0.35, and the diagnostic accuracy was 92.8%(309/333). The positive and negative predictive value were 11/16 and 94.0%(298/317), respectively. Conclusions: Routine contrast esophagram after three-incision esophagectomy with cervical anastomosis has low sensitivity and high specificity in the diagnosis of AL. The diagnostic time of AL is the 9^th day after surgery. It is necessary to prolong the observation time clinically, and combine RCE with CT, endoscopy and other inspection methods for diagnosis.

Inosine monophosphate dehydrogenase type1 sustains tumor growth in hepatocellular carcinoma

Background

Inosine monophosphate dehydrogenase (IMPDH) is the key enzyme in the biosynthesis of purine nucleotides. IMPDH1 and IMPDH2 are the two isoforms of IMPDH and they share 84% amino acid similarity and virtually indistinguishable catalytic activity. Although high expression of IMPDH2 has been reported in various cancers, the roles of IMPDH1 in hepatocellular carcinoma (HCC) are largely unknown.

Methods

The expression and the clinical relevance of IMPDH1 in 154 HCC patients were detected by immunohistochemistry analysis. The stable IMPDH1 knockdown HuH7 cells were established by lentiviral RNAi approach. The single cell proliferation was detected by colony‐forming unit assay. The tumor initiation and growth ability were measured by using xenograft tumor model in immunodeficient mice. The effect of IMPDH1 on cellular signaling pathways was analyzed by genome‐wide transcriptomic profiling.

Results

The expression of IMPDH1 is upregulated in tumor tissue compared with adjacent liver tissue, and higher expression of IMPDH1 is associated with better patient cumulative survival. In experimental models, loss of IMPDH1 in HCC cells inhibits the ability of single cell colony formation in vitro, and reduces the efficiency of tumor initiation and growth in immunodeficient mice. Consistently, loss of IMPDH1 results in distinct alterations of signaling pathways revealed by genome‐wide transcriptomic profiling.

Conclusion

IMPDH1 sustains HCC growth and progression.

An overview of solutions for airborne viral transmission reduction related to HVAC systems including liquid desiccant air-scrubbing

The spread of the coronavirus SARS-CoV-2 affects the health of people and the economy worldwide. As air transmits the virus, heating, ventilation and air-conditioning (HVAC) systems in buildings, enclosed spaces and public transport play a significant role in limiting the transmission of airborne pathogens at the expenses of increased energy consumption and possibly reduced thermal comfort. On the other hand, liquid desiccant technology could be adopted as an air scrubber to increase indoor air quality and inactivate pathogens through temperature and humidity control, making them less favourable to the growth, proliferation and infectivity of microorganisms. The objectives of this study are to review the role of HVAC in airborne viral transmission, estimate its energy penalty associated with the adoption of HVAC for transmission reduction and understand the potential of liquid desiccant technology. Factors affecting the inactivation of pathogens by liquid desiccant solutions and possible modifications to increase their heat and mass transfer and sanitising characteristics are also described, followed by an economic evaluation. It is concluded that the liquid desiccant technology could be beneficial in buildings (requiring humidity control or moisture removal in particular when viruses are likely to present) or in high-footfall enclosed spaces (during virus outbreaks).

[Effects of synonymous codon usage bias on mRNA half-life and translational regulation]

With the widespread application of genomics and transcriptomics in the genetics and cell biology of different species, synonymous codon usage bias has been gradually accepted and used to study the deep connection between biological evolution and biological phenotypes. It is an important part of the life activities that mRNA is expressed into proteins with normal biological activities. The synonymous codon usage patterns, which were named as 'the second genetic codon', can express genetic information carried by themselves at the levels of transcriptional regulations, translational regulations and metabolic activities through molecular mechanisms such as fine-tune translation selection. Some studies have shown that the length of mRNA half-life has significant impacts on mRNA activity and the process of transcription and translation. This review summarized the roles of synonymous codon usage patterns in transcription, translational regulation and post-translational modification, with the aim to better understand how organisms skillfully utilize the genetic effects caused by codon usage patterns to accurately synthesize different types of proteins, so as to ensure the growth or differentiation of the specific gene expression procedures to carry out smoothly and maintain the normal life cycle.

[Transglutaminase 2 inhibits the proliferation of H1 subtype influenza virus in MDCK cells]

Transglutaminase 2 (TGM2) is a ubiquitous multifunctional protein, which is related to the adhesion of different cells and tumor formation. Previous studies found that TGM2 is involved in the interaction between host cells and viruses, but the effect of TGM2 on the proliferation of influenza virus in cells has not been reported. To explore the effect of TGM2 during H1N1 subtype influenza virus infection, a stable MDCK cell line with TGM2 overexpression and a knockout cell line were constructed. The mRNA and protein expression levels of NP and NS1 as well as the virus titer were measured at 48 hours after pot-infection with H1N1 subtype influenza virus. The results showed that overexpression of TGM2 effectively inhibited the expression of NP and NS1 genes of H1N1 subtype influenza virus, while knockout of TGM2 up-regulated the expression of the NP and NS1 genes, and the expression of the NP at protein level was consistent with that at mRNA level. Virus proliferation curve showed that the titer of H1N1 subtype influenza virus decreased significantly upon TGM2 overexpression. On the contrary, the virus titer in TGM2 knockout cells reached the peak at 48 h, which further proved that TGM2 was involved in the inhibition of H1N1 subtype influenza virus proliferation in MDCK cells. By analyzing the expression of genes downstream of influenza virus response signaling pathway, we found that TGM2 may inhibit the proliferation of H1N1 subtype influenza virus by promoting the activation of JAK-STAT molecular pathway and inhibiting RIG-1 signaling pathway. The above findings are of great significance for revealing the mechanism underlying the interactions between host cells and virus and establishing a genetically engineering cell line for high-yield influenza vaccine production of influenza virus.

Estimating Global Prevalence of Metabolic Dysfunction-Associated Fatty Liver Disease in Overweight or Obese Adults

BACKGROUND & AIMS

Metabolic dysfunction-associated fatty liver disease (MAFLD) is a new terminology updated from non-alcoholic fatty liver disease (NAFLD). In this study, we aim to estimate the global prevalence of MAFLD specifically in overweight and obese adults from the general population by performing a systematic review and meta-analysis through mining the existing epidemiological data on fatty liver disease.

METHODS

We searched Medline, Embase, Web of Science, Cochrane and google scholar database from inception to November, 2020. DerSimonian-Laird random-effects model with Logit transformation was performed for data analysis. Sensitivity analysis and meta-regression were used to explore predictors of MAFLD prevalence in pooled statistics with high heterogeneity.

RESULTS

We identified 116 relevant studies comprised of 2,667,052 participants in general population with an estimated global MAFLD prevalence as 50.7% (95% CI 46.9-54.4) among overweight/obese adults regardless of diagnostic techniques. Ultrasound was the most commonly used diagnostic technique generating prevalence rate of 51.3% (95% CI, 49.1-53.4). Male (59.0%; 95% CI, 52.0-65.6) had a significantly higher MAFLD prevalence than female (47.5%; 95% CI, 40.7-54.5). Interestingly, MAFLD prevalence rates are comparable based on classical NAFLD and non-NAFLD studies in general population. The pooled estimate prevalence of comorbidities such as type 2 diabetes and metabolic syndrome was 19.7% (95% CI, 12.8-29.0) and 57.5% (95% CI, 49.9-64.8), respectively.

CONCLUSIONS

MAFLD has an astonishingly high prevalence rate in overweight and obese adults. This calls for attention and dedicated action from primary care physicians, specialists, health policy makers and the general public alike.

Recapitulating hepatitis E virus-host interactions and facilitating antiviral drug discovery in human liver-derived organoids

Hepatotropic viruses naturally have narrow host and tissue tropisms, challenging the development of robust experimental models. The advent of organoid technology provides a unique opportunity for moving the field forward. Here, we demonstrate that three-dimensional cultured organoids from fetal and adult human liver with cholangiocyte or hepatocyte phenotype support hepatitis E virus (HEV) replication. Inoculation with infectious HEV particles demonstrates that human liver–derived organoids support the full life cycle of HEV infection. By directing organoids toward polarized monolayers in a transwell system, we observed predominantly apical secretion of HEV particles. Genome-wide transcriptomic and tRNAome analyses revealed robust host responses triggered by viral replication. Drug screening in organoids identified brequinar and homoharringtonine as potent HEV inhibitors, which are also effective against the ribavirin resistance variant harboring G1634R mutation. Thus, successful recapitulation of HEV infection in liver-derived organoids shall facilitate the study of virus-host interactions and development of antiviral therapies.

[Pediatric SMARCB1/INI1-deficient poorly differentiated chordoma of the skull base: report of five cases and review of literature]

Objective: To investigate the clinicopathological characteristics and differential diagnosis of pediatric SMARCB1/INI1-deficient poorly differentiated chordoma (PDC) of the skull base. Methods: Five cases of SMARCB1/INI1-deficient PDC were identified in 139 cases of chordoma diagnosed in Sanbo Brain Institute, Capital Medical University, Beijing, China from March 2017 to March 2021. The clinical and imaging data of the 5 PDCs were collected. H&E and immunohistochemical staining, and DNA methylation array were used, and the relevant literatures were reviewed. Results: All 5 PDCs were located at the clivus. The average age of the patients was 6.4 years, ranging from 3 to 16 years. Three patients were female and two were male. Morphologically, in contrast with classical chordomas, they presented as epithelioid or spindle tumor cells organized in sheets or nests, with necrosis, active mitoses, and infiltration into surrounding tissue. All cases showed positivity of CKpan, EMA, vimentin and brachyury (nuclear stain), and loss of nuclear SMARCB1/INI1 expression. S-100 protein expression was not frequent (2/5). Ki-67 proliferative index was high (20%-50%). All cases had over-expressed p53. It was necessary to differentiate SMARCB1/INI1-dificient PDC from SMARCB1/INI1-dificient tumors occurring at skull base of children or the tumors with epithelial and spindle cell morphological features. The 3 PDCs with DNA methylation testing showed the methylation profiles different from the pediatric atypical teratoid/rhabdoid tumors. They formed an independent methylation profile cluster. The clinical prognosis of the 5 patients was poor, and the overall survival time was 2-17 months. Conclusions: PDC is a special subtype of chordoma, which often affects children and occurs in the clivus. The PDC shares epithelioid or spindle cell morphologic features which are different from the classic chordoma. Besides the typical immunohistochemical profile of chordoma, PDC also has loss of nuclear SMARCB1/INI1 expression and distinct epigenetic characteristics.

Estimating the global prevalence of hepatitis E virus in swine and pork products

Zoonotic transmission of hepatitis E virus (HEV), in particular the genotype (GT) 3 and GT4 strains, constitutes a major one health issue. Swine serves as an important reservoir and the processed pork products essentially contribute to foodborne transmission. This study comprehensively estimated HEV prevalence in domestic pigs, wild boars, and pork products. At global level, we found nearly 60% domestic pigs and 27% wild boars have ever encountered HEV infection based seroprevalence rate. Nearly 13% domestic and 9.5% wild swine are actively infected based on HEV RNA positivity. Importantly, about 10% of commercial pork products are HEV RNA positive, although available data are limited in this respect. Our results indicate the high prevalence rate of HEV infection in pigs and widespread contamination in pork products, although there are substantial variations at regional and country levels. These findings are important for better understanding the global epidemiology and clinical burden of HEV infection in human population related to zoonotic transmission.

The Burden of Colorectal Cancer Attributable to Diet Low in Fiber from 1990 to 2019: A Global, Regional and National Analysis

OBJECTIVES

The colorectal cancer (CRC) burden is increasingly high. The aim of this study was to investigate temporal and geographical trends in CRC deaths and disability-adjusted life-years (DALYs) attributable to diet low in fiber globally from 1990 to 2019.

DESIGN

Cross-sectional study.

SETTING

The study based on the Global Burden of Disease Study (GBD) 2019.

PARTICIPANTS

The population comprised individuals from 204 countries and territories who were diagnosed with CRC attributable to diet low in fiber from 1990 to 2019.

MEASUREMENTS

Deaths, DALYs, age-standardized mortality rates (ASMR), and age-standardized DALY rates (ASDR) for CRC attributable to diet low in fiber were described, and estimated annual percentage change (EAPC) was further calculated to assess the burden in different regions, countries, sexes, and age groups. Additionally, we explored the association between EAPC and ASMR/ASDR (in 1990) and Human Development Index (HDI, in 2019).

RESULTS

From 1990 to 2019, global ASMR and ASDR for CRC attributable to diet low in fiber decreased slightly, but the corresponding deaths and DALYs increased by 63.37% and 51.36%, respectively. Those burden varied considerably between regions and countries. The burden was higher in high, high-middle and middle SDI regions, especially in Asia and Western Europe, but when HDI > 0.7, an increasingly rapid decline in ASMR and ASDR was revealed. Unexpectedly, many less well-developed countries within the traditionally low deaths and DALYs regions of Africa, Central Latin America, and Middle East showed gradual increases in ASMR and ASDR.

CONCLUSION

The global burden of CRC attributable to diet low in fiber has decreased over the last 30 years, but remains at a high level. It is essential for decision-makers to take targeted measures for improving population awareness and intake of dietary fiber.

Hepatitis E virus infection activates NOD-like receptor family pyrin domain-containing 3 inflammasome antagonizing interferon response but therapeutically targetable

BACKGROUND AND AIMS

HEV infection is the most common cause of liver inflammation, but the pathogenic mechanisms remain largely unclear. We aim to explore whether HEV infection activates inflammasomes, crosstalk with antiviral interferon response, and the potential of therapeutic targeting.

APPROACH AND RESULTS

We measured IL-1β secretion, the hallmark of inflammasome activation, in serum of HEV-infected patients and rabbits, and in cultured macrophage cell lines and primary monocyte-derived macrophages. We found that genotypes 3 and 4 HEV infection in rabbits elevated IL-1β production. A profound increase of IL-1β secretion was further observed in HEV-infected patients (1,733 ± 1,234 pg/mL; n = 70) compared to healthy persons (731 ± 701 pg/mL; n = 70). Given that macrophages are the drivers of inflammatory response, we found that inoculation with infectious HEV particles robustly triggered NOD-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome activation in primary macrophages and macrophage cell lines. We further revealed that the ORF2 capsid protein and the formed integral viral particles are responsible for activating inflammasome response. We also identified NF-κB signaling activation as a key upstream event of HEV-induced NLRP3 inflammasome response. Interestingly, inflammasome activation antagonizes interferon response to facilitate viral replication in macrophages. Pharmacological inhibitors and clinically used steroids can effectively target inflammasome activation. Combining steroids with ribavirin simultaneously inhibits HEV and inflammasome response without cross-interference.

CONCLUSIONS

HEV infection strongly activates NLRP3 inflammasome activation in macrophages, which regulates host innate defense and pathogenesis. Therapeutic targeting of NLRP3, in particular when combined with antiviral agents, represents a viable option for treating severe HEV infection.

Host Non-Coding RNA Regulates Influenza A Virus Replication

Outbreaks of influenza, caused by the influenza A virus (IAV), occur almost every year in various regions worldwide, seriously endangering human health. Studies have shown that host non-coding RNA is an important regulator of host-virus interactions in the process of IAV infection. In this paper, we comprehensively analyzed the research progress on host non-coding RNAs with regard to the regulation of IAV replication. According to the regulation mode of host non-coding RNAs, the signal pathways involved, and the specific target genes, we found that a large number of host non-coding RNAs directly targeted the PB1 and PB2 proteins of IAV. Nonstructural protein 1 and other key genes regulate the replication of IAV and indirectly participate in the regulation of the retinoic acid-induced gene I-like receptor signaling pathway, toll-like receptor signaling pathway, Janus kinase signal transducer and activator of transcription signaling pathway, and other major intracellular viral response signaling pathways to regulate the replication of IAV. Based on the above findings, we mapped the regulatory network of host non-coding RNAs in the innate immune response to the influenza virus. These findings will provide a more comprehensive understanding of the function and mechanism of host non-coding RNAs in the cellular anti-virus response as well as clues to the mechanism of cell-virus interactions and the discovery of antiviral drug targets.

Series representations and simulations of isotropic random fields in the Euclidean space

This paper introduces the series expansion for homogeneous, isotropic and mean square continuous random fields in the Euclidean space, which involves the Bessel function and the ultraspherical polynomial, but differs from the spectral representation in terms of the ordinary spherical harmonics that has more terms at each level.The series representation provides a simple and efficient approach for simulation of isotropic (non-Gaussian) random fields.

Comparative assessment of favipiravir and remdesivir against human coronavirus NL63 in molecular docking and cell culture models

Human coronavirus NL63 (HCoV-NL63) mainly affects young children and immunocompromised patients, causing morbidity and mortality in a subset of patients. Since no specific treatment is available, this study aims to explore the anti-SARS-CoV-2 agents including favipiravir and remdesivir for treating HCoV-NL63 infection. We first successfully modelled the 3D structure of HCoV-NL63 RNA-dependent RNA polymerase (RdRp) based on the experimentally solved SARS-CoV-2 RdRp structure. Molecular docking indicated that favipiravir has similar binding affinities to SARS-CoV-2 and HCoV-NL63 RdRp with LibDock scores of 75 and 74, respectively. The LibDock scores of remdesivir to SARS-CoV-2 and HCoV-NL63 were 135 and 151, suggesting that remdesivir may have a higher affinity to HCoV-NL63 compared to SARS-CoV-2 RdRp. In cell culture models infected with HCoV-NL63, both favipiravir and remdesivir significantly inhibited viral replication and production of infectious viruses. Overall, remdesivir compared to favipiravir is more potent in inhibiting HCoV-NL63 in cell culture. Importantly, there is no evidence of resistance development upon long-term exposure to remdesivir. Furthermore, combining favipiravir or remdesivir with the clinically used antiviral cytokine interferon-alpha resulted in synergistic effects. These findings provided a proof-of-concept that anti-SARS-CoV-2 drugs, in particular remdesivir, have the potential to be repurposed for treating HCoV-NL63 infection.

Estimating the burden and modeling mitigation strategies of pork-related hepatitis E virus foodborne transmission in representative European countries

Hepatitis E virus (HEV) is an emerging zoonotic pathogen posing global health burden, and the concerns in Europe are tremendously growing. Pigs serve as a main reservoir, contributing to pork-related foodborne transmission. In this study, we aim to specifically simulate this foodborne transmission route and to assess potential interventions. We firstly established a dose-response relationship between the risk of transmission to human and the amount of ingested viruses. We further estimated the incidence of HEV infection specifically attributed to pork-related foodborne transmission in four representative European countries. Finally, we demonstrated a proof-of-concept of mitigating HEV transmission by implementing vaccination in human and pig populations. Our modeling approach bears essential implications for better understanding the transmission of pork-related foodborne HEV and for developing mitigation strategies.

Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.

Distinct effectiveness in containing COVID-19 epidemic: Comparative analysis of two cities in China by mathematical modeling

For better preparing future epidemic/pandemic, important lessons can be learned from how different parts of China responded to the early COVID-19 epidemic. In this study, we comparatively analyzed the effectiveness and investigated the mechanistic insight of two highly representative cities of China in containing this epidemic by mathematical modeling. Epidemiological data of Wuhan and Wenzhou was collected from local health commission, media reports and scientific literature. We used a deterministic, compartmental SEIR model to simulate the epidemic. Specific control measures were integrated into the model, and the model was calibrated to the recorded number of hospitalized cases. In the epicenter Wuhan, the estimated number of unisolated or unidentified cases approached 5000 before the date of city closure. By implementing quarantine, a 40% reduction of within-population contact was achieved initially, and continuously increased up to 70%. The expansion of emergency units has finally reduced the mean duration from disease onset to hospital admission from 10 to 3.2 days. In contrast, Wenzhou is characterized as an emerging region with large number of primarily imported cases. Quick response effectively reduced the duration from onset to hospital admission from 20 to 6 days. This resulted in reduction of R values from initial 2.3 to 1.6, then to 1.1. A 40% reduction of contact through within-population quarantine further decreased R values until below 1 (0.5; 95% CI: 0.4-0.65). Quarantine contributes to 37% and reduction of duration from onset to hospital admission accounts for 63% to the effectiveness in Wenzhou. In Wuhan, these two strategies contribute to 54% and 46%, respectively. Thus, control measures combining reduction of duration from disease onset to hospital admission and within-population quarantine are effective for both epicenters and settings primarily with imported cases.

Viral polymerase binding and broad-spectrum antiviral activity of molnupiravir against human seasonal coronaviruses

Endemic seasonal coronaviruses cause morbidity and mortality in a subset of patients, but no specific treatment is available. Molnupiravir is a promising pipeline antiviral drug for treating SARS-CoV-2 infection potentially by targeting RNA-dependent RNA polymerase (RdRp). This study aims to evaluate the potential of repurposing molnupiravir for treating seasonal human coronavirus (HCoV) infections. Molecular docking revealed that the active form of molnupiravir, β-D-N⁴-hydroxycytidine (NHC), has similar binding affinity to RdRp of SARS-CoV-2 and seasonal HCoV-NL63, HCoV-OC43 and HCoV-229E. In cell culture models, treatment of molnupiravir effectively inhibited viral replication and production of infectious viruses of the three seasonal coronaviruses. A time-of-drug-addition experiment indicates the specificity of molnupiravir in inhibiting viral components. Furthermore, combining molnupiravir with the protease inhibitor GC376 resulted in enhanced antiviral activity. Our findings highlight that the great potential of repurposing molnupiravir for treating seasonal coronavirus infected patients.

Correlation between culprit vessel/tirofiban and reperfusion bradyarrhythmia in patients with ST-segment elevation myocardial infarction after emergency PCI

OBJECTIVE

To evaluate the correlation between culprit vessel/tirofiban and reperfusion bradyarrhythmia in patients with ST-segment elevation myocardial infarction (STEMI) after emergency percutaneous coronary intervention (PCI).

PATIENTS AND METHODS

A total of 123 STEMI patients undergoing emergency PCI in our hospital from September 2018 to September 2019 were selected and divided into the reperfusion arrhythmias (RA) group (50 cases) and non-RA group (NRA, 73 cases) according to whether RA occurring during PCI. The baseline data such as age and underlying disease were statistically analyzed. Then, the differences were compared between the two groups. According to whether reperfusion bradyarrhythmia (RB) occurring during PCI, 123 STEMI patients were divided into the RB group (63 cases) and non-RB group (60 cases). The relation between culprit vessel/tirofiban and RB was analyzed. ROC curves analysis and multivariate logistic regression were conducted for the risk factors of RA and RB.

RESULTS

Among 123 patients with STEMI after PCI treatment, 73 patients had RA (59.35%), including RB 63 cases and tachyarrhythmia 10 cases. Results of single factor analysis showed that there was statistical significance in 3 factors including the patient age, infarction area and vascular blood flow TIMI classification between RA group and NRA group (p<0.05). ROC curve analysis indicated that the continuous variable patent ages had predictive value in the prevalence of RA, which resulting in an AUC 0.624 and a cut-off pointed age 57 (sensitivity 72.60, specificity 52.00). Multivariate regression analysis showed that the patient age (>57 years old), infarction area in inferior wall and grade 0 lesion vascular blood flow TIMI classification in RA group was significantly higher than that in NRA group (p<0.05). Tirofiban was not associated with RB in STEMI patients treated with emergency PCI, while culprit vessel was statistically significant between RB group and NRB group (p<0.05). Multivariate regression analysis indicated that culprit vessel of the right coronary artery and grade 0 lesions vascular blood flowed TIMI classification was independent risk factors to occurring RB in the STEMI patients with emergency PCI.

CONCLUSIONS

Tirofiban was not associated with RB in STEMI patients treated with emergency PCI. However, it may increase the risk of RB development when the culprit vessel is the right coronary artery. Therefore, timely corresponding treatments and reduction of reperfusion damage are of great significance for those patients.

Inhibiting pyrimidine biosynthesis impairs Peste des Petits Ruminants Virus replication through depletion of nucleoside pools and activation of cellular immunity

Replication of peste des petits ruminants virus (PPRV) strongly depends on the cellular environment and resources of host cells including nucleoside pool. Thus, enzymes involved in nucleoside biosynthesis (such as pyrimidine biosynthesis pathway) are regarded as attractive targets for antiviral drug development. Here, we demonstrate that brequinar (BQR) and leflunomide (LFM) which are two specific inhibitors of DHODH enzyme and 6-azauracil (6-AU) which is an ODase enzyme inhibitor robustly inhibit PPRV replication in HEK293T cell line as well as in peripheral blood mononuclear cells isolated from goat. We further demonstrate that these agents exert anti-PPRV activity via the depletion of purimidine nucleotide. Interestingly, these inhibitors can trigger the transcription of antiviral interferon-stimulated genes (ISGs). However, the induction of ISGs is largely independent of the classical JAK-STAT pathway. Combination of BQR with interferons (IFNs) exerts enhanced ISG induction and anti-PPRV activity. Taken together, this study reveals an unconventional novel mechanism of crosstalk between nucleotide biosynthesis pathways and cellular antiviral immunity in inhibiting PPRV replication. In conclusion, targeting pyrimidine biosynthesis represents a potential strategy for developing antiviral strategies against PPRV.

Effects of intermittent fasting on liver physiology and metabolism in mice

A broad spectrum of health benefits from intermittent fasting have been reported in studies on animal models and human subjects. However, the underlying mechanisms of these beneficial effects remain largely elusive. The present study aimed to explore the effects and potential mode of action of intermittent fasting in mouse models with a focus on the liver. C57BL/6 mice were subjected to intermittent fasting or ad libitum feeding as controls. It was determined that 12 h of daily intermittent fasting for 30 days significantly reduced the cumulative food intake compared with that in mice with ad libitum feeding. Fasting resulted in a significantly reduced liver mass but only had a minimal effect on bodyweight. The effects on the liver by 30 days of fasting were not reversed by subsequent ad libitum refeeding for 30 days. Among the measured blood biochemical parameters, the levels of blood glucose were decreased, while the levels of alkaline phosphatase were increased in fasting mice. Of note, targeted metabolic profiling revealed global elevation of metabolites in the livers of fasting mice. These metabolic molecules included adenosine triphosphate, nicotinamide adenine dinucleotide phosphate (NADP), reduced NADP and succinate, which are essentially involved in the citric acid cycle and oxidative phosphorylation. Thus, it was concluded that daily 12 h of intermittent fasting for one month significantly reduced the liver weight of mice, which is associated with enhanced liver metabolism.

Cell-based influenza vaccine: current production, halal status assessment, and recommendations towards Islamic-compliant manufacturing

Influenza virus is a life-threatening pathogen that infects millions of people every year, with annual mortality in the hundreds of thousands. The scenario for controlling infection has worsened with increasing numbers of vaccine hesitancy cases reported worldwide due to objections on safety, religious and other grounds. Uses of haram (impermissible) and mashbooh (doubtful) ingredients in vaccine production has raised doubts among Muslim consumers and consequently stimulated serious vaccine hesitancy. To address this major problem, we have reviewed and recommended some alternatives appropriate for manufacturing cell-based influenza vaccine which comply with Islamic laws and consumers' needs. Intensive assessments of current influenza vaccine production in both scientific and Islamic views have led to the identification of four main ingredients deemed impermissible in novel sharia-compliant (approved by Islamic laws) vaccine manufacturing. Only some of these impermissible components could be replaced with halal (permissible) alternatives, while others remain impermissible due to unavailability and unsuitability.

Prevalence and clinical features of hepatitis E virus infection in pregnant women: A large cohort study in Inner Mongolia, China

BACKGROUND AND AIM

Hepatitis E virus (HEV) infection causes severe maternal and fetal outcomes in pregnant women. These patients are exclusively from resource-limited regions with genotype 1 HEV infection, but not from western countries with genotype 3 prevalence. Since the circulating strains in China have evolved from the waterborne genotype 1 to the zoonotic genotype 4 HEV in the past decades, this study aims to evaluate the prevalence and clinical features of HEV infection in a large cohort of pregnant women in Inner Mongolia, China.

METHODS

A total of 3278 pregnant women who visited the Inner Mongolia Maternal and Child Care hospital during 2018 were enrolled. Serum samples were examined for anti-HEV IgG and anti-HEV IgM antibodies using ELISA. Demographic information, results of clinical biochemical tests, maternal and neonatal outcomes were collected.

RESULTS

Among the recruited 3278 pregnant women, 6.0% were anti-HEV IgG antibody positive, 0.3% were anti-HEV IgM antibody positive and 0.3% were positive for both anti-HEV IgG and anti-HEV IgM antibodies. HEV viral RNA was not detected. Pregnant women with recent/ongoing HEV infection indicated by anti-HEV IgM positivity have slightly higher ALT level, and potential risk of developing hyperlipidemia, preterm delivery and neonatal jaundice.

CONCLUSIONS

These findings indicated that HEV infection is associated with a possible increase in adverse maternal, fetal and neonatal outcomes in our cohort. Thus, the burden of HEV infection in pregnant women in China appears distinct from resource-limited regions and western countries. Nevertheless, future studies are required to confirm and extend our findings.