Corrigendum: A metagenomic analysis of mosquito virome collected from different animal farms at Yunnan-Myanmar border of China

[This corrects the article DOI: 10.3389/fmicb.2020.591478.].

Survey of rectal cancer MRI technique and reporting tumour descriptors in the UK: a multi-centre British Society of Gastrointestinal and Abdominal Radiology (BSGAR) audit

AIM

To evaluate variation in magnetic resonance imaging (MRI) technique and reporting of rectal cancer staging examinations across the UK.

MATERIALS AND METHODS

A retrospective, multi-centre audit was undertaken of imaging protocols and information documented within consecutive MRI rectal cancer reports between March 2020 and August 2021, which were compared against American and European guidelines. Inclusion criteria included histologically proven rectal adenocarcinoma and baseline staging MRI rectum only.

RESULTS

Fully anonymised data from 924 MRI reports by 78 radiologists at 24 centres were evaluated. Thirty-two per cent of radiologists used template reporting, but these reports offered superior documentation of 13 out of 18 key tumour features compared to free-text reports including T-stage, relation to peritoneal reflection and mesorectal fascia (MRF), nodal status, and presence of extramural venous invasion (EMVI; p<0.027 in each). There was no significant differences in the remaining five features. Across all tumour locations, the tumour relationship to the MRF, the presence of EMVI, and the presence of tumour deposits were reported in 79.5%, 85.6%, and 44% of cases, respectively, and tumour, nodal, and distant metastatic stage documented in 94.4%, 97.7%, and 78.3%. In low rectal tumours, the relationship to the anal sphincter complex was reported in only 54.6%.

CONCLUSION

Considerable variation exists in rectal cancer MRI acquisition and reporting in this sample of UK centres. Inclusion of key radiological features in reports must be improved for risk stratification and treatment decisions. Template reporting is superior to free-text reporting. Routine adoption of standardised radiology practices should now be considered to improve standards to facilitate personalised precision treatment for patients to improve outcomes.

The role of diffusion-weighted MRI in the accurate diagnosis of vertebral compression fractures: A comparative study

INTRODUCTION

Accurately distinguishing between benign and malignant vertebral compression fractures is crucial for clinical management. This study evaluated the predictive accuracy of diffusion-weighted imaging (DWI) in differentiating the cause of vertebral fractures using MRI.

METHODS

A longitudinal cross-over study was conducted at Jinnah Postgraduate Medical Centre (JPMC) Karachi from July 2018 to January 2021. Patients with vertebral compression fractures underwent T1-weighted, T2-weighted, and DWI imaging with ADC mapping on a 1.5 T MRI scanner. Imaging findings were compared with histopathologic results and clinical follow-up. Sensitivity, specificity, and ROC curve analyses were performed.

RESULTS

The study enrolled 303 patients with a mean age of 43.6 ± 10.9 years, of whom 118 were male. DWI demonstrated high accuracy in predicting the cause of vertebral compression fractures, with a sensitivity of 96.2 %, a specificity of 76.2 %, and an area under the ROC curve of 0.857. The optimal ADC cut-off value was 0.82 × 10˄-3 mm˄2/s, which yielded a positive predictive value of 79.7 % and a negative predictive value of 95.4 %.

CONCLUSIONS

DWI is a safe and non-invasive imaging modality with excellent predictive accuracy in differentiating between benign and malignant vertebral compression fractures. Iso- or hypointensity of collapsed vertebral bodies on DWI suggests a benign lesion, while T2-weighted hyperintensity is highly indicative of malignancy. Low signal on ADC is also highly indicative of malignant vertebral fractures. Incorporating DWI improves accuracy in assessing vertebral lesions, especially when standard sequences are inconclusive.

IMPLICATIONS FOR PRACTICE

DWI revolutionizes vertebral compression fracture diagnosis, distinguishing between benign and malignant cases. This precision guides treatment decisions, minimizing the necessity for invasive procedures like biopsy. As a safe and reliable imaging method, DWI elevates patient care, ensuring accurate diagnostics and improved outcomes.

NS2B-D55E and NS2B-E65D Variations are Responsible for Differences in NS2B-NS3 Protease Activities Between Japanese Encephalitis Virus Genotype I and III in Fluorogenic Peptide Model

Japanese Encephalitis Virus (JEV) NS2B-NS3 is a protein complex composed of NS3 proteases and a NS2B cofactor. The N-terminal protease domain (180 residues) of NS3 (NS3(pro)) interacts directly with a central 40-amino acid hydrophilic domain of NS2B (NS2B(H)) to form an active serine protease. In this study, the recombinant NS2B(H)-NS3(pro) proteases were prepared in E. coli and used to compare the enzymatic activity between genotype I (GI) and III (GIII) NS2B-NS3 proteases. The GI NS2B(H)-NS3(pro) was able to cleave the sites at internal C, NS2A/NS2B, NS2B/NS3 and NS3/NS4A junctions that were identical to the sites proteolytically processed by GIII NS2B(H)-NS3(pro). Analysis of the enzymatic activity of recombinant NS2B(H)-NS3(pro) proteases using a model of fluorogenic peptide substrate revealed that the proteolytical processing activity of GIII NS2B(H)-NS3(pro) was significantly higher than that of GI NS2B(H)-NS3(pro). There were eight amino acid variations between GI and GIII NS2B(H)-NS3(pro), which may be responsible for the difference in enzymatic activities between GI and GIII proteases. Therefore, recombinant mutants were generated by exchanging NS2B(H) and NS3(pro) domains between GI and GIII NS2B(H)-NS3(pro) and subjected to protease activity analysis. Substitution of NS2B(H) significantly altered the protease activities, as compared to the parental NS2B(H)-NS3(pro), suggesting that NS2B(H) played an essential role in regulation of NS3(pro) protease activity. To further identify the amino acids responsible for the difference in protease activities, multiple substitution mutants including the individual and combined mutations at the variant residue 55 and 65 of NS2B(H) were generated and subjected to protease activity analysis. Replacement of NS2B-55 and NS2B-65 of GI to GIII significantly increased the enzymatic activity of GI NS2B(H)-NS3(pro) protease, whereas mutation of NS2B-55 and NS2B-65 of GIII to GI remarkably reduced the enzymatic activity of GIII NS2B(H)-NS3(pro) protease. Overall, these data demonstrated that NS2B-55 and NS2B-65 variations in hydrophilic domain of NS2B co-contributed to the difference in NS2B(H)-NS3(pro) protease activities between GI and GIII. These observations gain an insight into the role of NS2B in regulation of NS3 protease activities, which is useful for understanding the replication of JEV GI and GIII viruses.

Optimized protocol for mouse footpad immune cell isolation for single-cell RNA sequencing and flow cytometry

Single-cell RNA sequencing (scRNA-seq) requires the preparation of a highly viable single-cell suspension to get reliable sequencing results. Here, we present a protocol for isolating mouse footpad leukocytes while maintaining high viability. We describe steps for footpad collection, enzymatic tissue dissociation, leukocyte isolation and purification, and cell fixation and preservation. We then detail combinatorial barcoding, library preparation, scRNA-seq, and data analysis. Cells can be used to generate a complete molecular atlas at the single cell level.

Imaging manifestations of IgG4-related disease

IgG4-related disease is a multisystem immune-mediated disorder associated with lesions manifesting an IgG4-rich plasma cell infiltrate and often raised serum IgG4 concentrations. The disease can mimic neoplastic, infective, and inflammatory processes due to features such as development of masses or organ enlargement. Prompt consideration of this diagnosis is essential to avoid unnecessary investigations and offer appropriate treatments, which can include steroids and other immunosuppressive agents. Although histology is typically diagnostic, imaging is critical to assess disease burden, determine biopsy targets, and evaluate response to treatment. Characteristic imaging features can also point towards the diagnosis in the absence of biopsy. This review highlights these features, as well as more atypical findings, grouped by organ or system. Differential diagnoses are emphasised. The full spectrum of imaging methods is discussed. Whole-body imaging with integrated 2-[18F]-fluoro-2-deoxy-d-glucose (FDG) positron-emission tomography (PET)/computed tomography (CT) has an evolving role in the detection of multi-organ involvement and subsequent follow-up.

Palmitoylation at Residue C221 of Japanese Encephalitis Virus NS2A Protein Contributes to Viral Replication Efficiency and Virulence

Palmitoylation of viral proteins is crucial for host-virus interactions. In this study, we examined the palmitoylation of Japanese encephalitis virus (JEV) nonstructural protein 2A (NS2A) and observed that NS2A was palmitoylated at the C221 residue of NS2A. Blocking NS2A palmitoylation by introducing a cysteine-to-serine mutation at C221 (NS2A/C221S) impaired JEV replication in vitro and attenuated the virulence of JEV in mice. NS2A/C221S mutation had no effect on NS2A oligomerization and membrane-associated activities, but reduced protein stability and accelerated its degradation through the ubiquitin-proteasome pathway. These observations suggest that NS2A palmitoylation at C221 played a role in its protein stability, thereby contributing to JEV replication efficiency and virulence. Interestingly, the C221 residue undergoing palmitoylation was located at the C-terminal tail (amino acids 195 to 227) and is removed from the full-length NS2A following an internal cleavage processed by viral and/or host proteases during JEV infection. IMPORTANCE An internal cleavage site is present at the C terminus of JEV NS2A. Following occurrence of the internal cleavage, the C-terminal tail (amino acids 195 to 227) is removed from the full-length NS2A. Therefore, it was interesting to discover whether the C-terminal tail contributed to JEV infection. During analysis of viral palmitoylated protein, we observed that NS2A was palmitoylated at the C221 residue located at the C-terminal tail. Blocking NS2A palmitoylation by introducing a cysteine-to-serine mutation at C221 (NS2A/C221S) impaired JEV replication in vitro and attenuated JEV virulence in mice, suggesting that NS2A palmitoylation at C221 contributed to JEV replication and virulence. Based on these findings, we could infer that the C-terminal tail might play a role in the maintenance of JEV replication efficiency and virulence despite its removal from the full-length NS2A at a certain stage of JEV infection.

Recent Population Dynamics of Japanese Encephalitis Virus

Japanese encephalitis virus (JEV) causes acute viral encephalitis in humans and reproductive disorders in pigs. JEV emerged during the 1870s in Japan, and since that time, JEV has been transmitted exclusively throughout Asia, according to known reporting and sequencing records. A recent JEV outbreak occurred in Australia, affecting commercial piggeries across different temperate southern Australian states, and causing confirmed infections in humans. A total of 47 human cases and 7 deaths were reported. The recent evolving situation of JEV needs to be reported due to its continuous circulation in endemic regions and spread to non-endemics areas. Here, we reconstructed the phylogeny and population dynamics of JEV using recent JEV isolates for the future perception of disease spread. Phylogenetic analysis shows the most recent common ancestor occurred about 2993 years ago (YA) (95% Highest posterior density (HPD), 2433 to 3569). Our results of the Bayesian skyline plot (BSP) demonstrates that JEV demography lacks fluctuations for the last two decades, but it shows that JEV genetic diversity has increased during the last ten years. This indicates the potential JEV replication in the reservoir host, which is helping it to maintain its genetic diversity and to continue its dispersal into non-endemic areas. The continuous spread in Asia and recent detection from Australia further support these findings. Therefore, an enhanced surveillance system is needed along with precautionary measures such as regular vaccination and mosquito control to avoid future JEV outbreaks.

Metabolic syndrome and aberrant immune responses to viral infection and vaccination: Insights from small animal models

This review outlines the propensity for metabolic syndrome (MetS) to induce elevated disease severity, higher mortality rates post-infection, and poor vaccination outcomes for viral pathogens. MetS is a cluster of conditions including high blood glucose, an increase in circulating low-density lipoproteins and triglycerides, abdominal obesity, and elevated blood pressure which often overlap in their occurrence. MetS diagnoses are on the rise, as reported cases have increased by greater than 35% since 1988, resulting in one-third of United States adults currently diagnosed as MetS patients. In the aftermath of the 2009 H1N1 pandemic, a link between MetS and disease severity was established. Since then, numerous studies have been conducted to illuminate the impact of MetS on enhancing virally induced morbidity and dysregulation of the host immune response. These correlative studies have emphasized the need for elucidating the mechanisms by which these alterations occur, and animal studies conducted as early as the 1940s have linked the conditions associated with MetS with enhanced viral disease severity and poor vaccine outcomes. In this review, we provide an overview of the importance of considering overall metabolic health in terms of cholesterolemia, glycemia, triglyceridemia, insulin and other metabolic molecules, along with blood pressure levels and obesity when studying the impact of metabolism-related malignancies on immune function. We highlight the novel insights that small animal models have provided for MetS-associated immune dysfunction following viral infection. Such animal models of aberrant metabolism have paved the way for our current understanding of MetS and its impact on viral disease severity, dysregulated immune responses to viral pathogens, poor vaccination outcomes, and contributions to the emergence of viral variants.

Immune response to arbovirus infection in obesity

Obesity is a global health problem that affects 650 million people worldwide and leads to diverse changes in host immunity. Individuals with obesity experience an increase in the size and the number of adipocytes, which function as an endocrine organ and release various adipocytokines such as leptin and adiponectin that exert wide ranging effects on other cells. In individuals with obesity, macrophages account for up to 40% of adipose tissue (AT) cells, three times more than in adipose tissue (10%) of healthy weight individuals and secrete several cytokines and chemokines such as interleukin (IL)-1β, chemokine C-C ligand (CCL)-2, IL-6, CCL5, and tumor necrosis factor (TNF)-α, leading to the development of inflammation. Overall, obesity-derived cytokines strongly affect immune responses and make patients with obesity more prone to severe symptoms than patients with a healthy weight. Several epidemiological studies reported a strong association between obesity and severe arthropod-borne virus (arbovirus) infections such as dengue virus (DENV), chikungunya virus (CHIKV), West Nile virus (WNV), and Sindbis virus (SINV). Recently, experimental investigations found that DENV, WNV, CHIKV and Mayaro virus (MAYV) infections cause worsened disease outcomes in infected diet induced obese (DIO) mice groups compared to infected healthy-weight animals. The mechanisms leading to higher susceptibility to severe infections in individuals with obesity remain unknown, though a better understanding of the causes will help scientists and clinicians develop host directed therapies to treat severe disease. In this review article, we summarize the effects of obesity on the host immune response in the context of arboviral infections. We have outlined that obesity makes the host more susceptible to infectious agents, likely by disrupting the functions of innate and adaptive immune cells. We have also discussed the immune response of DIO mouse models against some important arboviruses such as CHIKV, MAYV, DENV, and WNV. We can speculate that obesity-induced disruption of innate and adaptive immune cell function in arboviral infections ultimately affects the course of arboviral disease. Therefore, further studies are needed to explore the cellular and molecular aspects of immunity that are compromised in obesity during arboviral infections or vaccination, which will be helpful in developing specific therapeutic/prophylactic interventions to prevent immunopathology and disease progression in individuals with obesity.

A cross sectional survey on the effect of COVID-19 related restrictions on undergraduate and postgraduate medical education in Qatar

BACKGROUND

COVID-19 pandemic has affected all dimensions of day to day life across the world and medical education was no exception. With this study, we aimed to understand the effect of nationwide restrictions on medical education in Qatar, the models of education adopted during this period and perceptions of participants to the same.

METHODS

We conducted a cross-sectional study utilizing an online questionnaire distributed via convenience sampling between April-October 2020. Study participants were faculty and trainees in governmental undergraduate and postgraduate medical education institutes. Two sets of questionnaires were designed for each group. They were asked a series of questions to assess pre- and post-COVID pandemic educational practices, their preferred teaching methods, and their familiarity with electronic teaching platforms. Faculty respondents were asked about their perceived barriers to delivery of medical education during the pandemic and their agreement on a 5-point Likert scale on specific elements. Trainees were asked a series of multiple-choice questions to characterize their pre- and post-COVID pandemic educational experiences. Both groups were asked open-ended questions to provide qualitative insights into their answers. Data were analysed using STATA software version 12.0.

RESULTS

Majority of trainees (58.5%) responded that the pandemic has adversely affected medical education at both the undergraduate and postgraduate levels. Trainees (58.5%) and faculty (35.7%) reported an increased reliance on e-learning. Trainees preferred face-to-face education, while faculty preferred a combination of models of education delivery (33.5% versus 37.1%, p = 0.38). Although 52.5% of the faculty had no previous experience of delivering education through e-learning modalities, 58.9% however felt confident in using e-learning software.

CONCLUSIONS

Faculty and trainees agree that the COVID-19 pandemic has had a significant impact on the provision of medical education and training in Qatar, with an increased dependence on e-learning. As trainee's prefer face-to-face models of education, we may have to consider restructuring of medical curricula in order to ensure that optimum learning is achieved via e-learning, while at the same time enhancing our use, knowledge and understanding of the e -learning methods. Further research is warranted to assess if these changes have influenced objective educational outcomes like graduation rates or board scores.

Potential Role of Flavivirus NS2B-NS3 Proteases in Viral Pathogenesis and Anti-flavivirus Drug Discovery Employing Animal Cells and Models: A Review

Flaviviruses are known to cause a variety of diseases in humans in different parts of the world. There are very limited numbers of antivirals to combat flavivirus infection, and therefore new drug targets must be explored. The flavivirus NS2B-NS3 proteases are responsible for the cleavage of the flavivirus polyprotein, which is necessary for productive viral infection and for causing clinical infections; therefore, they are a promising drug target for devising novel drugs against different flaviviruses. This review highlights the structural details of the NS2B-NS3 proteases of different flaviviruses, and also describes potential antiviral drugs that can interfere with the viral protease activity, as determined by various studies. Moreover, optimized in vitro reaction conditions for studying the NS2B-NS3 proteases of different flaviviruses may vary and have been incorporated in this review. The increasing availability of the in silico and crystallographic/structural details of flavivirus NS2B-NS3 proteases in free and drug-bound states can pave the path for the development of promising antiflavivirus drugs to be used in clinics. However, there is a paucity of information available on using animal cells and models for studying flavivirus NS2B-NS3 proteases, as well as on the testing of the antiviral drug efficacy against NS2B-NS3 proteases. Therefore, on the basis of recent studies, an effort has also been made to propose potential cellular and animal models for the study of flavivirus NS2B-NS3 proteases for the purposes of exploring flavivirus pathogenesis and for testing the efficacy of possible drugs targets, in vitro and in vivo.

Potential Role of Birds in Japanese Encephalitis Virus Zoonotic Transmission and Genotype Shift

Japanese encephalitis (JE) is a vaccine-preventable disease caused by the Japanese encephalitis virus (JEV), which is primarily prevalent in Asia. JEV is a Flavivirus, classified into a single serotype with five genetically distinct genotypes (I, II, III, IV, and V). JEV genotype III (GIII) had been the most dominant strain and caused numerous outbreaks in the JEV endemic countries until 1990. However, recent data shows the emergence of JEV genotype I (GI) as a dominant genotype and it is gradually displacing GIII. The exact mechanism of this genotype displacement is still unclear. The virus can replicate in mosquito vectors and vertebrate hosts to maintain its zoonotic life cycle; pigs and aquatic wading birds act as an amplifying/reservoir hosts, and the humans and equines are dead-end hosts. The important role of pigs as an amplifying host for the JEV is well known. However, the influence of other domestic animals, especially birds, that live in high abundance and close proximity to the human is not well studied. Here, we strive to briefly highlight the role of birds in the JEV zoonotic transmission, discovery of birds as a natural reservoirs and amplifying host for JEV, species of birds susceptible to the JEV infection, and the proposed effect of JEV on the poultry industry in the future, a perspective that has been neglected for a long time. We also discuss the recent in vitro and in vivo studies that show that the newly emerged GI viruses replicated more efficiently in bird-derived cells and ducklings/chicks than GIII, and an important role of birds in the JEV genotype shift from GIII to GI.

A Metagenomic Analysis of Mosquito Virome Collected From Different Animal Farms at Yunnan-Myanmar Border of China

Metagenomic analysis of mosquito-borne and mosquito-specific viruses is useful to understand the viral diversity and for the surveillance of pathogens of medical and veterinary importance. Yunnan province is located at the southwest of China and has rich abundance of mosquitoes. Arbovirus surveillance is not conducted regularly in this province particularly at animal farms, which have public health as well as veterinary importance. Here, we have analyzed 10 pools of mosquitoes belonging to Culex tritaeniorhyncus, Aedes aegypti, Anopheles sinensis, and Armigeres subalbatus species, collected from different animal farms located at Yunnan province of China by using metagenomic next-generation sequencing technique. The generated viral metagenomic data reveal that the viral community matched by the reads was highly diverse and varied in abundance among animal farms, which contained more than 19 viral taxonomic families, specific to vertebrates, invertebrates, fungi, plants, protozoa, and bacteria. Additionally, a large number of viral reads were related to viruses that are non-classified. The viral reads related to animal viruses included parvoviruses, anelloviruses, circoviruses, flaviviruses, rhabdoviruses, and seadornaviruses, which might be taken by mosquitoes from viremic animal hosts during blood feeding. Notably, the presence of viral reads matched with Japanese encephalitis virus, Getah virus, and porcine parvoviruses in mosquitoes collected from different geographic sites suggested a potential circulation of these viruses in their vertebrate hosts. Overall, this study provides a comprehensive knowledge of diverse viral populations present at animal farms of Yunnan province of China, which might be a potential source of diseases for humans and domestic animals.

Analyses of mitogenomic markers shed light on the divergence, population dynamics, and demographic history of Pakistani chickens

Pakistan is one of a few sites, associated with the earliest known independent domestication event in the evolutionary history of chicken, which is socio-economically and historically the most important poultry bird in the country. However, the divergence, past population dynamics, and demographic history of Pakistani chickens have not been addressed so far. Therefore, we herein investigated the indigenous Pakistani chickens using mitogenomic markers. We first prepared individual DNA samples from the chicken feathers, and generated nucleotide sequence data, which was then subjected to various population genetics analyses. In molecular phylogenetic analysis, the Pakistani chickens were clustered under nine different clades. Among the wild fowls, the Indian red jungle fowl (IRJF) shared very close affinities to Pakistani chickens. The Bayesian skyline plot showed an increase in the effective population size of Pakistani chickens during the last 50 years. Finally, a time-calibrated phylogeny inferred molecular divergence of the Pakistani chickens. A molecular rate of 3.6 × 10^-6 mutations/site/year (95% HPD interval: 2.28 × 10^-8 to 9.32 × 10^-6) was estimated for the data set. In a rooted tree with root-age of 12058 years (95% HPD interval: 1161-38411), the Pakistani chicken haplotypes showed divergence from IRJF haplotypes around 6987 years (95% HPD interval: 1132-20746) ago, and they shared their most recent common ancestor with Gallus gallus spadiceus, and G. g. jabouillei at the root of the tree. Overall, these results suggest that Pakistani chicken haplotypes share their ancestral gene pool with the IRJF as compared to other red jungle fowl subspecies.

Mosquito Defensins Enhance Japanese Encephalitis Virus Infection by Facilitating Virus Adsorption and Entry within the Mosquito

Japanese encephalitis virus (JEV) is a viral zoonosis that can cause viral encephalitis, death, and disability. Although the Culex mosquito is the primary vector of JEV, little is known about JEV transmission by this kind of mosquito. Here, we found that mosquito defensin facilitated the adsorption of JEV on target cells via the defensin/lipoprotein receptor-related protein 2 (LRP2) axis. Mosquito defensin bound the ED III domain of the viral envelope (E) protein and directly mediated efficient virus adsorption on the target cell surface; the receptor LRP2, which is expressed on the cell surface, affected defensin-dependent adsorption. As a result, mosquito defensin enhanced JEV infection in the salivary gland, increasing the possibility of viral transmission by mosquitoes. These findings demonstrate the novel role of mosquito defensin in JEV infection and the mechanisms through which the virus exploits mosquito defensin for infection and transmission.IMPORTANCE In this study, we observed the complex roles of mosquito defensin in JEV infection; mosquito defensin exhibited a weak antiviral effect but strongly enhanced binding. In the latter, defensin directly binds the ED III domain of the viral E protein and promotes the adsorption of JEV to target cells by interacting with lipoprotein receptor-related protein 2 (LRP2), thus accelerating virus entry. Together, our results indicate that mosquito defensin plays an important role in facilitating JEV infection and potential transmission.

Detection of Japanese encephalitis virus in mosquitoes from Xinjiang during next-generation sequencing arboviral surveillance

A total of 548 mosquitoes were collected from different animal farms located near to highly populated cities in Xinjiang and were subjected to metagenomic next-generation sequencing (mNGS). The mNGS data demonstrated that 18,842 (XJ1 strain) and 1,077 (XJ2 strain) of Japanese encephalitis virus (JEV)-related reads were detected in XJ1 and XJ2 mosquito samples collected from Wushi and Wensu counties of Aksu area, which accounted for 0.032% and 0.006% of the total clean reads generated from XJ1 and XJ2 samples, respectively. The Bayesian molecular phylogenetic analysis suggested that XJ1 and XJ2 strains belonged to JEV genotype III and were clustered with JEV strains isolated in China. Notably, Bayesian molecular time line phylogeny revealed that XJ1 strain shared its MRCA with JEV GSS strain about 67 YA, suggesting that XJ1 strain likely originated from linages closely related to GSS strain and spread to Xinjiang later. Overall, these findings suggest that Xinjiang was probably not free from JEV, and thus, a further surveillance of JEV is required in Xinjiang.

Performance of cell-free tumor DNA testing for 101 clinical laboratories on College of American Pathologists proficiency tests

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Background: Cell-free tumor DNA or circulating tumor DNA tests are increasingly used in clinical care to detect somatic mutations from solid tumors. However, data on laboratory performance characteristics using standardized samples is limited. Methods: Well-characterized reference materials were used for the College of American Pathologists (CAP) cell-free tumor DNA proficiency testing surveys, which consisted of stabilized DNA fragmented to simulate cell-free DNA in a synthetic plasma matrix. For the 2018A, 2018B, 2019A and 2019B surveys, laboratories tested for hotspot mutations (single and dinucleotide sequence changes) in EGFR, BRAF, KRAS, NRAS, and IDH1 at variant allele fractions ranging from 0.1% - 1.0%. As per CAP proficiency testing standards, results were scored according to the known mutation(s) engineered at designated variant allele fractions in each PT sample. Nine laboratories were excluded from analysis because they provided incomplete results. Statistical significance was calculated using a multivariate logistic regression model. Results: In 2018 and 2019, 101 laboratories submitted survey results for at least one proficiency testing mailing. There were 5088 total proficiency testing responses for EGFR, BRAF, KRAS, NRAS, and IDH1 mutations across 12 different samples. For the 3585 responses submitted for BRAF, KRAS, NRAS, and IDH1, sensitivity ranged from 94.6 – 100%, while specificity exceeded 99%. There were no significant differences in performance between analytical methodologies for BRAF, KRAS, NRAS, and IDH1 mutations. Performance characteristics for EGFR mutations among the 1503 responses showed a combined sensitivity of 87.1% and specificity of 98.7%. For laboratories detecting mutations in EGFR, next-generation sequencing methods exhibited a sensitivity (true positivity) of 95.7% while the sensitivity of non-NGS methods was lower at 81.7% ( P= 0.02). Conclusions: These findings demonstrate high sensitivity and specificity for clinical laboratories performing cell-free tumor DNA tests. For EGFR mutations, NGS outperformed non-NGS methods. These data suggest excellent overall agreement among laboratories performing clinical cell-free tumor DNA tests. Further investigation across variant allele fractions and additional variant types is warranted.

Phenotypic and Genotypic Comparison of a Live-Attenuated Genotype I Japanese Encephalitis Virus SD12-F120 Strain with Its Virulent Parental SD12 Strain

The phenotypic and genotypic characteristics of a live-attenuated genotype I (GI) strain (SD12-F120) of Japanese encephalitis virus (JEV) were compared with its virulent parental SD12 strain to gain an insight into the genetic changes acquired during the attenuation process. SD12-F120 formed smaller plaque on BHK-21 cells and showed reduced replication in mouse brains compared with SD12. Mice inoculated with SD12-F120 via either intraperitoneal or intracerebral route showed no clinical symptoms, indicating a highly attenuated phenotype in terms of both neuroinvasiveness and neurovirulence. SD12-F120 harbored 29 nucleotide variations compared with SD12, of which 20 were considered silent nucleotide mutations, while nine resulted in eight amino acid substitutions. Comparison of the amino acid variations of SD12-F120 vs. SD12 pair with those from other four isogenic pairs of the attenuated and their virulent parental strains revealed that the variations at E¹³⁸ and E¹⁷⁶ positions of E protein were identified in four and three pairs, respectively, while the remaining amino acid variations were almost unique to their respective strain pairs. These observations suggest that the genetic changes acquired during the attenuation process were likely to be strain-specific and that the mechanisms associated with JEV attenuation/virulence are complicated.

Rapid differential detection of genotype I and III Japanese encephalitis virus from clinical samples by a novel duplex TaqMan probe-based RT-qPCR assay

Japanese Encephalitis (JE) is an acute infectious disease that threatens both human and pig populations throughout Asia. JE is caused by the Japanese Encephalitis Virus (JEV), of which genotype III (GIII) had been the most prevalent strain throughout Asia, but recent studies have shown that genotype I (GI) has replaced GIII as the predominant version. Pigs and mosquitoes play a primary role in JEV transmission. However, a method for the rapid differentiation between JEV G I and G III remains unavailable. This study aimed to establish a rapid JEV genotyping method using novel duplex TaqMan RT-qPCR assay.specific primer and probes located in the PrM/M gene that were able to specifically differentiate GI and GIII JEV, was selected as the duplex TaqMan RT-qPCR target.The specificity, sensitivity and reproducibility test of this assay were validated. The sensitivity of the assay was 10 genomic RNA copies for both GI and GIII JEV in field mosquito and pig samples,and more sensitive than the current methods. In addition, the novel assay can be completed in less than 1 h. Therefore, This duplex TaqMan RT-qPCR assay is a promising tool for rapid differential detection and epidemiology of GI and GIII JEV strains in China. The results showed that co-circulation of GI and GIII infections with GI infection being more prevalent in pigs or mosquitoes in eastern China.

Establishment and characterization of the pig tonsil epithelial (PT) cell line as a new model for persist infection of Japanese Encephalitis Virus

Japanese encephalitis virus (JEV) causes a serious zoonotic disease worldwide, pig is the reservoir and amplifying host of JEV. JEV can persist infect tonsil in pig, but the relation between persist infection in tonsil and reservoir are not clear until now. A stable pig tonsil cell line is necessary for JEV persist infection research. In this study, we established a continuous epithelial cell line, named PT cell, from the pig tonsil. This cell is susceptible to JEV. We determined the growth characteristics, molecular properties, microstructure profiles of PT cell. JEV is easy to enter PT cell which may partly explain the reason of persist infection. We further determined that LMAN2L, a mannose lectin proteins, is the primary viral receptors for JEV entry in PT cell. IFITM3, an cellular surface antiviral factor, is underexpression in PT cell after JEV infection. All these results provide solid evidence that PT cell will promote additional research on JEV persist infection in pig tonsil.

Antiviral activity of phage display-selected peptides against Japanese encephalitis virus infection in vitro and in vivo

Japanese Encephalitis virus (JEV) is a zoonotic flavivirus that is the most significant etiological agent of childhood viral neurological infections. However, no specific antiviral drug is currently available to treat JEV infections. The JEV envelope (E) protein is a class II viral fusion protein that mediates host cell entry, making interference with the interaction between the E protein of JEV and its cognate receptors an attractive strategy for anti-JEV drug development. In this study, we identified a peptide derived from a phage display peptide library against the E protein of JEV, designated P1, that potentially inhibits in vitro and in vivo JEV infections. P1 inhibits JEV infection in BHK-21 cells with 50% inhibitory capacity at a concentration of 35.9 μM. The time-of-addition assay indicates that JEV replication is significantly inhibited during pre-infection and co-infection of P1 with JEV while post-infection treatments with P1 have very little impact on JEV proliferation, showing that P1 inhibits JEV infection at early stages and indicating the potential prophylactic effect of P1. We adapted an in vitro BiFC assay system and demonstrated that P1 interacts with JEV E proteins and blocks their entry into cells. We also evaluated the therapeutic efficacy of P1 in a lethal JEV mouse model exhibiting systemic and brain infections. Interestingly, P1 treatment protected C57BL/6 mice against mortality, markedly reduced the viral loads in blood and brain, and diminished the histopathological lesions in the brain cells. In addition to controlling systemic infection, P1 has a very low level of cytotoxicity and acts in a sequence-specific manner, as scrambled peptide sP1 does not show any antiviral activity. In conclusion, our in vitro and in vivo experimental findings show that P1 possesses antiviral activity against JEV infections, is safe to use, and has potential for further development as an antiviral treatment against JEV infections.

A viral metagenomic analysis reveals rich viral abundance and diversity in mosquitoes from pig farms

Mosquitoes harbour a diversity of viruses and are responsible for several mosquito-borne viral diseases of humans and animals, thereby leading to major public health concerns, and significant economic losses across the globe. Viral metagenomics offers a great opportunity for bulk analysis of viral genomes retrieved directly from environmental samples. In this study, we performed a viral metagenomic analysis of five pools of mosquitoes belonging to Aedes, Anopheles and Culex species, collected from different pig farms in the vicinity of Shanghai, China, to explore the viral community carried by mosquitoes. The resulting metagenomic data revealed that viral community in the mosquitoes was highly diverse and varied in abundance among pig farms, which comprised of more than 48 viral taxonomic families, specific to vertebrates, invertebrates, plants, fungi, bacteria and protozoa. In addition, a considerable number of viral reads were related to viruses that are not classified by host. The read sequences related to animal viruses included parvoviruses, anelloviruses, circoviruses, flavivirus, rhabdovirus and seadornaviruses, which might be taken up by mosquitoes from viremic animal hosts during blood feeding. Notably, sample G1 contained the most abundant sequence related to Banna virus, which is of public health interest because it causes encephalitis in humans. Furthermore, non-classified viruses also shared considerable virus sequences in all the samples, presumably belonging to unexplored virus category. Overall, the present study provides a comprehensive knowledge of diverse viral populations carried by mosquitoes at pig farms, which is a potential source of diseases for mammals including humans and animals. These viral metagenomic data are valuable for assessment of emerging and re-emerging viral epidemics.

The emerged genotype I of Japanese encephalitis virus shows an infectivity similar to genotype III in Culex pipiens mosquitoes from China

Japanese Encephalitis virus (JEV) is a zoonotic flavivirus that represents the most significant etiology of childhood viral neurological infections throughout the Asia. During the last 20 years, JEV genotype dominance has shifted from genotype III (GIII) to genotype I (GI). To date, the exact mechanism of this displacement is still not known. Culex (Cx.) mosquitoes are the most common species in China and play an essential role in maintaining JEV enzootic transmission cycle. In this study, we used Cx. pipiens mosquitoes from China as an in vivo mosquito model to explore if mosquitoes played a potential role in JEV genotype shift. We exposed female Cx. pipiens mosquitoes orally to either GI or GIII JEV strains. Midgut, whole mosquitoes, secondary organs, and salivary glands of JEV-infected mosquitoes were collected at 7 and 14 days of post infection (dpi) and subjected to measure the infection rate, replication kinetics, dissemination rate and transmission potential of the infected JEV strains in Cx. pipiens mosquitoes by 50% tissue culture infective dose assay. We found that Cx. pipiens mosquito was competent vector for both GI and GIII JEV infection, with similar infection rates and growth kinetics. After the establishment of infection, Cx. pipiens mosquitoes disseminated both JEV genotypes to secondary organs at similar rates of dissemination. A few GI-infected mosquito salivary glands (16.2%) were positive for GI virus, whereas GIII virus was undetectable in GIII-infected mosquito salivary glands at 7 dpi. However, 29.4% (5/17) and 36.3% (8/22) were positive for GI- and GIII-infected mosquito salivary glands at 14 dpi, respectively, showing an increase in JEV positive rate. No statistical difference in the transmission rate between GI- and GIII-infected mosquitoes was detected. Our experiment data demonstrated that GI and GIII viruses have similar infectivity in Cx. pipiens mosquitoes, suggesting that Cx. pipiens mosquitoes from China may not play a critical role in JEV genotype shift. Although the current data were obtained solely from Cx. pipiens mosquitoes, it is likely that the conclusion drawn could be extrapolated to the role of mosquitoes in JEV genotype shift.

Research progress on the composition and function of parasite-derived exosomes

Parasites use excretory-secretory pathways to communicate with the host. Characterization of exosomes within the excretory-secretory products reveal by which parasites manipulate their hosts. Parasite derived exosomes provide a mechanistic framework for protein and miRNAs transfer. Transcriptomics and proteomics of parasite exosomes identified a large number of miRNAs and proteins being utilized by parasites in their survival, reproduction and development. Characterization of proteins and miRNAs in parasite secreted exosomes provide important information on host-parasite communication and forms the basis for future studies. In this review, we summarize recent advances in isolation and molecular characterization (protein and miRNAs) of parasite derived exosomes.

Critical care usage after major gastrointestinal and liver surgery: a prospective, multicentre observational study

BACKGROUND

Patient selection for critical care admission must balance patient safety with optimal resource allocation. This study aimed to determine the relationship between critical care admission, and postoperative mortality after abdominal surgery.

METHODS

This prespecified secondary analysis of a multicentre, prospective, observational study included consecutive patients enrolled in the DISCOVER study from UK and Republic of Ireland undergoing major gastrointestinal and liver surgery between October and December 2014. The primary outcome was 30-day mortality. Multivariate logistic regression was used to explore associations between critical care admission (planned and unplanned) and mortality, and inter-centre variation in critical care admission after emergency laparotomy.

RESULTS

Of 4529 patients included, 37.8% (n=1713) underwent planned critical care admissions from theatre. Some 3.1% (n=86/2816) admitted to ward-level care subsequently underwent unplanned critical care admission. Overall 30-day mortality was 2.9% (n=133/4519), and the risk-adjusted association between 30-day mortality and critical care admission was higher in unplanned [odds ratio (OR): 8.65, 95% confidence interval (CI): 3.51-19.97) than planned admissions (OR: 2.32, 95% CI: 1.43-3.85). Some 26.7% of patients (n=1210/4529) underwent emergency laparotomies. After adjustment, 49.3% (95% CI: 46.8-51.9%, P<0.001) were predicted to have planned critical care admissions, with 7% (n=10/145) of centres outside the 95% CI.

CONCLUSIONS

After risk adjustment, no 30-day survival benefit was identified for either planned or unplanned postoperative admissions to critical care within this cohort. This likely represents appropriate admission of the highest-risk patients. Planned admissions in selected, intermediate-risk patients may present a strategy to mitigate the risk of unplanned admission. Substantial inter-centre variation exists in planned critical care admissions after emergency laparotomies.

Role of water chemistry and stabilizers on the Vero-cells-based infectivity of Newcastle disease virus live vaccine

Newcastle disease virus (NDV) live vaccines are supplied in lyophilized form and usually administered through conventional routes (drinking water, spray, or eye drop) following reconstitution in a diluent. Virus inactivation due to physico-chemical properties of the diluent at the time of administration may lead to vaccine failure. The present study aimed to evaluate the survival of NDV live vaccine strain immersed in 5 pH-amended water samples (pH 5.00, pH 6.00, pH 7.00, pH 8.00, and pH 9.00) by sequential determination of virus infectivity on Vero cells for 3 hours. Minimum reduction in virus infectivity was recorded in the water with neutral or slightly alkaline pH, while the virus was relatively less stable at extreme pH conditions. Maximum reduction of infectivity was observed in the water with pH 9.00 in which the virus was completely inactivated within 3 hours. Addition of stabilizers (Cevamune^® or skimmed milk) slightly altered the pH and total dissolved solids (TDS) values of the virus-charged water samples. In the stabilizer-added water samples, minimum reduction in infectivity was observed in the water with neutral pH, followed by the ones with a pH of 8.00, 6.00, 5.00, and 9.00. In all types of water samples, T-90 values (time required for 90% reduction in virus infectivity) were highest (485 minutes) at neutral pH (pH 7.00) and lowest (102 to 134 min) at an extreme alkaline condition (pH 9.00). Results of the present study indicate that water with a pH range of 7.00 to 8.00 is suitable for administration of NDV live vaccines. However, the addition of Cevamune^® or skimmed milk may have beneficial effects on preserving the infectivity of the virus, even at extreme pH conditions.

A phase Ib/II study of imatinab and everolimus in patients with PDGFRA+ synovial sarcoma

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Background: Our group previously reported that PDGFRA is the most highly overexpressed kinase gene in synovial sarcoma. Our preclinical studies also demonstrated synergistic anti-tumor activity by inhibiting both PDGFRA and mTOR signaling with imatinib and rapamycin respectively in PDGFRA + synovial sarcoma cell lines. Based on these data, a phase Ib/II study to evaluate the toxicity and efficacy of imatinib and everolimus was undertaken. Methods: The primary endpoint of the phase 1b portion of the study was to determine the maximum tolerated dose (MTD) of everolimus administered with imatinib. Starting dose of everolimus and imatinib was 5 mg/day and 400 mg/day respectively. Response rate (RR) by RECIST was the primary end-point of the Phase II study. The phase II study used a Simon two stage design. 9 patients (pts) were to be accrued initially. If there were no responses, further accrual would be stopped and treatment declared ineffective. If there was at least 1 response, an additional 15 pts would be accrued for a total of 24. Key eligibility: metastatic disease, any number of priors. Pre and post treatment tumor biopsies were mandated. Results: 12 pts were treated.5 M and 7 F, median age 44 (range: 22-71), median priors 4 (range: 0 - 6). Two DLTs were observed at dose level 2 (10 mg everolimus /400 mg imatinib) with grade 3 transaminases and hypophosphatemia. Everolimus 5 mg/ imatinib 400 mg was the MTD in the phase II study. 10 pts evaluable for response, included 4 pts treated at the MTD in the Phase 1b study. There were no RECIST responses. Stable disease was observed in 3 pts (7, 7, 19 mos.). Western blot and IHC analysis of matched pair tumor biopsies indicate inhibition of p-AKT, p-S6 and decreases in Ki 67. Conclusions: Imatinib and everolimus failed to achieve its primary response endpoint. However, prolonged stable disease in 3 pts in association with inhibition of PDGFRA and mTOR suggest clinical benefit and biological effect for this drug combination. Clinical trial information: CTEP 8603.

Pancreatic injuries after blunt abdominal trauma: an analysis of 110 patients treated at a level 1 trauma centre

BACKGROUND AND OBJECTIVE

Injuries to the pancreas are uncommon, but may result in considerable morbidity and mortality. This study evaluated the management of blunt pancreatic injuries using a previously defined protocol to determine which factors predicted morbidity and mortality.

METHODS

The study design was a retrospective chart review of all adult patients with blunt pancreatic injuries treated at a level 1 trauma centre between March 1981 and June 2009.

RESULTS

One hundred and ten patients (92 men, 18 women; mean age 30 years, range 13-68 years) were treated during the study period. Forty-six patients had American Association for the Surgery of Trauma (AAST) grade 1 or 2 pancreatic injuries and 64 had AAST grade 3, 4 or 5 pancreatic injuries. Injuries involved the head (N=21), neck (N=15), body (N=48) and tail (N=26) of the pancreas. The mean number of organs injured was 2.7 per patient (range 1-4). One hundred and one patients underwent a total of 123 operations, including drainage of the pancreatic injury (N=73), distal pancreatectomy (N=39) and Whipple resection (N=5). The overall complication rate was 74.5% and the mortality rate 16.4%. Only 2 of the 18 deaths were attributable to the pancreatic injury. Shock on presentation was highly predictive of death; 17 of 39 patients with shock died, compared with 1 of 71 patients who were not shocked (p < 0.0001). Fourteen of 46 patients with grade 1 and 2 pancreatic injuries died compared with 4 of 64 patients with grades 3, 4 and 5 injuries (p < 0.001). Mortality increased exponentially as the number of associated injuries increased. Two of 57 patients with injury to the pancreas only or one associated injury died, compared with 16 of 53 with two or more associated injuries (p < 0.0013).

CONCLUSIONS

This study demonstrated a significant correlation between the AAST grade of injury and pancreas-specific morbidity and between shock on admission, the number of associated injuries and death, in patients with blunt pancreatic injuries. Although morbidity and mortality rates after blunt pancreatic trauma are high, death was usually the result of major associated injuries and not related to the pancreatic injury.

P16 as a marker to differentiate atypical lipomatous tumor/well-differentiated liposarcoma from deep seated lipoma: An immunohistochemical analysis of 51 cases

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Background: Atypical lipomatous tumor (ALT)/well-differentiated (WD) liposarcoma is a locally aggressive malignant mesenchymal neoplasm characterized by supernumerary ring and giant marker chromosomes with amplification of MDM2 gene. These cytogenetic characteristics can be very helpful to distinguish ALT from deep-seated lipomas. As ALTs have only rare presence of lipoblasts, they can resemble benign lipomas rendering difficulty in morphological diagnosis. P16INK4 is a specific inhibitor of CDK4/CDK6. CDK6 gene is often found co-amplified with MDM2 gene in ALTs. P16 overexpression is a hallmark of cervical dysplasia. Our study investigates the value of p16 expression in cytogenetically confirmed ALTs and deep-seated lipomas. Design: Fifty-one (51) cases of lipomatous neoplasms, with cytogenetic results, from forty-three (43) patients were collected for the study from the archives in department of pathology, UMDNJ/NJMS during 1998 - 2005. These include 18 cases of deep-seated lipoma, one hibernoma, and 32 cases of ALT / well-differentiated liposarcoma (24 patients, five patients with recurrence, and four cases with de-differentiation). Immunohistochemical staining for p16 was performed on representative paraffin blocks. Staining results were scored according to intensity (negative 0, weak 1+, intermediate 2+, and strong 3+) and percentage of positive cells. Results: Twenty-eight cases (28/32, 87.5%) of ALT/WD liposarcoma, including all four cases of dedifferentiated liposarcoma, showed strong nuclear p16 expression. In cases of recurrence, the primary and recurrent tumor showed the same pattern of p16 staining. Four cases (4/32, 12.5%) of ALT/WD liposarcoma showed negative p16 expression. All cases of deep-seated lipoma (18/18, 100%) and single hibernoma showed negative p16 staining except focal positivity in areas of fat necrosis in two cases (p16 positivity, 87.5 vs. 0%, P <0.00001, Fisher's exact test). Conclusion: 1). P16 appears to be a valuable marker to differentiate ALT and deep-seated lipomas. 2). P16 expression remains unchanged in progression and transformation of ALT. 3). P16 related signal transduction pathway most likely is an early event in tumorogenesis of ALT.

No significant financial relationships to disclose.