Correction: Kosoltanapiwat et al. A Novel Simian Adenovirus Associating with Human Adenovirus Species G Isolated from Long-Tailed Macaque Feces. Viruses 2023, 15, 1371.

After publication of the article, the authors received comments from a member of the Viruses editorial board who is an expert in the field of adenovirus concerning figures and references that should be included in the paper [...].

Ex vivo drug sensitivity screening predicts response to temozolomide in glioblastoma patients and identifies candidate biomarkers.

BACKGROUND: Patient-derived glioma stem-like cells (GSCs) have become the gold-standard in neuro-oncological research; however, it remains to be established whether loss of in situ microenvironment affects the clinically-predictive value of this model. We implemented a GSC monolayer system to investigate in situ-in vitro molecular correspondence and the relationship between in vitro and patient response to temozolomide (TMZ). METHODS: DNA/RNA-sequencing was performed on 56 glioblastoma tissues and 19 derived GSC cultures. Sensitivity to TMZ was screened across 66 GSC cultures. Viability readouts were related to clinical parameters of corresponding patients and whole-transcriptome data. RESULTS: Tumour DNA and RNA sequences revealed strong similarity to corresponding GSCs despite loss of neuronal and immune interactions. In vitro TMZ screening yielded three response categories which significantly correlated with patient survival, therewith providing more specific prediction than the binary MGMT marker. Transcriptome analysis identified 121 genes related to TMZ sensitivity of which 21were validated in external datasets. CONCLUSION: GSCs retain patient-unique hallmark gene expressions despite loss of their natural environment. Drug screening using GSCs predicted patient response to TMZ more specifically than MGMT status, while transcriptome analysis identified potential biomarkers for this response. GSC drug screening therefore provides a tool to improve drug development and precision medicine for glioblastoma.

A Novel Simian Adenovirus Associating with Human Adeno-virus Species G Isolated from Long-Tailed Macaque Feces.

Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been identified using metagenomic analysis. In this study, a VIDISCA metagenomics workflow was used to identify potential unknown viruses in 33 fecal samples from asymptomatic long-tailed macaques (Macaca fascicularis) in Ratchaburi Province, Thailand. Putatively novel astroviruses, enteroviruses, and adenoviruses were detected and confirmed by PCR analysis of long-tailed macaque fecal samples collected from areas in four provinces, Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan, where humans and monkeys live in proximity (total n = 187). Astroviruses, enteroviruses, and adenoviruses were present in 3.2%, 7.5%, and 4.8% of macaque fecal samples, respectively. One adenovirus, named AdV-RBR-6-3, was successfully isolated in human cell culture. Whole-genome analysis suggested that it is a new member of the species Human adenovirus G, closely related to Rhesus adenovirus 53, with evidence of genetic recombination and variation in the hexon, fiber, and CR1 genes. Sero-surveillance showed neutralizing antibodies against AdV-RBR-6-3 in 2.9% and 11.2% of monkeys and humans, respectively, suggesting cross-species infection of monkeys and humans. Overall, we reported the use of metagenomics to screen for possible new viruses, as well as the isolation and molecular and serological characterization of the new adenovirus with cross-species transmission potential. The findings emphasize that zoonotic surveillance is important and should be continued, especially in areas where humans and animals interact, to predict and prevent the threat of emerging zoonotic pathogens.

Diversity and Long-Term Dynamics of Human Blood Anelloviruses.

Anelloviruses (AVs) are commensal members of the human blood virome. Even though it was estimated that over 90% of the human population carries AVs, the dynamics of the AV virome ("anellome") are unknown. We investigated the dynamics of blood anellomes in two healthy people followed up for more than 30 years. Both subjects were positive for AVs in the majority of samples. Alphatorquevirus (torque teno virus [TTV]) was the most common genus in both subjects, followed by Betatorquevirus (torque teno minivirus [TTMV]) and Gammatorquevirus (torque teno midivirus [TTMDV]). Almost five times more lineages were found in subject 1 than in subject 2, and the anellomes differed phylogenetically. Both anellomes remained compositionally stable, and 9 out of 64 AV lineages were detected in over half of the time points. We confirmed the long-term and short-term persistence of 13 lineages by specific quantitative PCR (qPCR). AV lineages were detected in blood for over 30 years. Noticeable differences in anellome richness were found between the tested subjects, but both anellomes remained compositionally stable over time. These findings demonstrate that the human blood anellome is personal and that AV infection is chronic and potentially commensal. IMPORTANCE Knowledge of the persistence of AVs in humans is crucial to our understanding of the nature of AV infection (chronic or acute) and the role of AV in the host. We therefore investigated the dynamics of anellovirus infection in two healthy people followed up for 30 years. Our findings suggest that the human blood anellovirus virome (anellome) remains stable and personal for decades.

Bromide strongly influences the formation of reaction products during the ozonation of diclofenac, metoprolol and isoproturon.

Bromide as an omnipresent matrix component in wastewater can react with ozone to form hypobromous acid (HOBr). This secondary oxidant can subsequently react with micropollutants but also with formed intermediates. Therefore, bromide and especially HOBr can highly influence the formation of transformation products (TPs). This has already been reported for the ozonation of N,N-dimethylsulfamide leading to the formation of the cancerogenic N-nitrosodimethylamine only in bromide containing waters. In this study, the influence of different bromide and ozone concentrations on the formation of TPs during the ozonation of isoproturon (ISO), metoprolol (METO) and diclofenac (DCF) were investigated. Additionally, TPs were identified, which are formed in the direct reaction of the micropollutants with HOBr with and without subsequent ozonation. The results showed that even if the reactions of ozone with the substances should be favored bromide can highly influence the formation of TPs already at low concentrations. In summary, new TPs after the reaction with HOBr (and subsequent ozonation) could be postulated for ISO, METO and DCF. This underlines that the present water matrix can have a high influence on the formation of TPs and that these mechanisms need to be investigated further.

Rectal bacteriome and virome signatures and clinical outcomes in community-acquired pneumonia: An exploratory study.

Background Bacterial intestinal communities interact with the immune system and may contribute to protection against community-acquired pneumonia (CAP). Intestinal viruses are closely integrated with these bacterial communities, yet the composition and clinical significance of these communities in CAP patients are unknown. The aims of this exploratory study were to characterise the composition of the rectal bacteriome and virome at hospital admission for CAP, and to determine if microbiota signatures correlate with clinical outcomes. Methods We performed a prospective observational cohort study in CAP patients, admitted to a university or community hospital in the Netherlands between October 2016 and July 2018, and controls. Rectal bacteriome and virome composition were characterised using 16S ribosomal RNA gene sequencing and virus discovery next-generation sequencing, respectively. Unsupervised multi-omics factor analysis was used to assess the co-variation of bacterial and viral communities, which served as primary predictor. The clinical outcomes of interest were the time to clinical stability and the length of hospital stay. Findings 64 patients and 38 controls were analysed. Rectal bacterial alpha (p = 0•0015) and beta diversity (r2 =0•023, p = 0•004) of CAP patients differed from controls. Bacterial and viral microbiota signatures correlated with the time to clinical stability (hazard ratio 0•43, 95% confidence interval 0•20-0•93, p = 0•032) and the length of hospital stay (hazard ratio 0•37, 95% confidence interval 0•17-0•81, p = 0•012), although only the latter remained significant following p-value adjustment for examining multiple candidate cut-points (p = 0•12 and p = 0•046, respectively). Interpretation This exploratory study provides preliminary evidence that intestinal bacteriome and virome signatures could be linked with clinical outcomes in CAP. Such exploratory data, when validated in independent cohorts, could inform the development of a microbiota-based diagnostic panel used to predict clinical outcomes in CAP. Funding Netherlands Organization for Scientific Research and Netherlands Organization for Health Research and Development.

Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness.

Bacterial microbiota play a critical role in mediating local and systemic immunity, and shifts in these microbial communities have been linked to impaired outcomes in critical illness. Emerging data indicate that other intestinal organisms, including bacteriophages, viruses of eukaryotes, fungi, and protozoa, are closely interlinked with the bacterial microbiota and their host, yet their collective role during antibiotic perturbation and critical illness remains to be elucidated. We employed multi-omics factor analysis (MOFA) to systematically integrate the bacterial (16S rRNA), fungal (intergenic transcribed spacer 1 rRNA), and viral (virus discovery next-generation sequencing) components of the intestinal microbiota of 33 critically ill patients with and without sepsis and 13 healthy volunteers. In addition, we quantified the absolute abundances of bacteria and fungi using 16S and 18S rRNA PCRs and characterized the short-chain fatty acids (SCFAs) butyrate, acetate, and propionate using nuclear magnetic resonance spectroscopy. We observe that a loss of the anaerobic intestinal environment is directly correlated with an overgrowth of aerobic pathobionts and their corresponding bacteriophages as well as an absolute enrichment of opportunistic yeasts capable of causing invasive disease. We also observed a strong depletion of SCFAs in both disease states, which was associated with an increased absolute abundance of fungi with respect to bacteria. Therefore, these findings illustrate the complexity of transkingdom changes following disruption of the intestinal bacterial microbiome.IMPORTANCE While numerous studies have characterized antibiotic-induced disruptions of the bacterial microbiome, few studies describe how these disruptions impact the composition of other kingdoms such as viruses, fungi, and protozoa. To address this knowledge gap, we employed MOFA to systematically integrate viral, fungal, and bacterial sequence data from critically ill patients (with and without sepsis) and healthy volunteers, both prior to and following exposure to broad-spectrum antibiotics. In doing so, we show that modulation of the bacterial component of the microbiome has implications extending beyond this kingdom alone, enabling the overgrowth of potentially invasive fungi and viruses. While numerous preclinical studies have described similar findings in vitro, we confirm these observations in humans using an integrative analytic approach. These findings underscore the potential value of multi-omics data integration tools in interrogating how different components of the microbiota contribute to disease states. In addition, our findings suggest that there is value in further studying potential adjunctive therapies using anaerobic bacteria or SCFAs to reduce fungal expansion after antibiotic exposure, which could ultimately lead to improved outcomes in the intensive care unit (ICU).

Matrix composition during ozonation of N-containing substances may influence the acute toxicity towards Daphnia magna.

Micropollutants reach the aquatic environment through wastewater treatment plant effluents. Ozonation, applied in wastewater treatment for micropollutants abatement, can yield transformation products (TP), which might be of ecotoxicological concern. Previous studies on TP formation were mostly performed in ultrapure water. However, the water matrix can have a substantial influence and lead to unpredictable yields of TPs with toxicological potential. In this study the acute toxicity (immobilization) of the parent substances (isoproturon and metoprolol) and also of available TPs of isoproturon, metoprolol and diclofenac towards Daphnia magna (D. magna) were investigated. Further, the acute toxicity of TP mixtures, formed during ozonation of isoproturon, metoprolol and diclofenac was evaluated in the following systems: in the presence of radical scavengers (tert-butanol and dimethyl sulfoxide) and in the presence of hypobromous acid (HOBr), a secondary oxidant in ozonation. For all tested substances and TP standards, except 2,6-dichloroaniline (EC50 1.02 mg/L (48 h)), no immobilization of D. magna was detected. Ozonated pure water and wastewater did not show an immobilization effect either. After ozonation of diclofenac in the presence of dimethyl sulfoxide 95% (48 h) of the daphnids were immobile. Ozonation of parent substances, after the reaction with HOBr, showed no effect for isoproturon but a high effect on D. magna for diclofenac (95% immobilization (48 h)) and an even higher effect for metoprolol (100% immobilization (48 h)). These results emphasize that complex water matrices can influence the toxicity of TPs as shown in this study for D. magna.

Seasonal coronavirus protective immunity is short-lasting.

A key unsolved question in the current coronavirus disease 2019 (COVID-19) pandemic is the duration of acquired immunity. Insights from infections with the four seasonal human coronaviruses might reveal common characteristics applicable to all human coronaviruses. We monitored healthy individuals for more than 35 years and determined that reinfection with the same seasonal coronavirus occurred frequently at 12 months after infection.

Patient-derived organoids can predict response to chemotherapy in metastatic colorectal cancer patients.

There is a clear and unmet clinical need for biomarkers to predict responsiveness to chemotherapy for cancer. We developed an in vitro test based on patient-derived tumor organoids (PDOs) from metastatic lesions to identify nonresponders to standard-of-care chemotherapy in colorectal cancer (CRC). In a prospective clinical study, we show the feasibility of generating and testing PDOs for evaluation of sensitivity to chemotherapy. Our PDO test predicted response of the biopsied lesion in more than 80% of patients treated with irinotecan-based therapies without misclassifying patients who would have benefited from treatment. This correlation was specific to irinotecan-based chemotherapy, however, and the PDOs failed to predict outcome for treatment with 5-fluorouracil plus oxaliplatin. Our data suggest that PDOs could be used to prevent cancer patients from undergoing ineffective irinotecan-based chemotherapy.

Stromal-derived interleukin 6 drives epithelial-to-mesenchymal transition and therapy resistance in esophageal adenocarcinoma.

Esophageal adenocarcinoma (EAC) has a dismal prognosis, and survival benefits of recent multimodality treatments remain small. Cancer-associated fibroblasts (CAFs) are known to contribute to poor outcome by conferring therapy resistance to various cancer types, but this has not been explored in EAC. Importantly, a targeted strategy to circumvent CAF-induced resistance has yet to be identified. By using EAC patient-derived CAFs, organoid cultures, and xenograft models we identified IL-6 as the stromal driver of therapy resistance in EAC. IL-6 activated epithelial-to-mesenchymal transition in cancer cells, which was accompanied by enhanced treatment resistance, migratory capacity, and clonogenicity. Inhibition of IL-6 restored drug sensitivity in patient-derived organoid cultures and cell lines. Analysis of patient gene expression profiles identified ADAM12 as a noninflammation-related serum-borne marker for IL-6-producing CAFs, and serum levels of this marker predicted unfavorable responses to neoadjuvant chemoradiation in EAC patients. These results demonstrate a stromal contribution to therapy resistance in EAC. This signaling can be targeted to resensitize EAC to therapy, and its activity can be measured using serum-borne markers.

Thyroid Ultrasound: More Sensitive than Radioactive Iodine Imaging in Detecting Recurrence of Papillary Thyroid Cancer in Two Pediatric Patients.

BACKGROUND: Papillary thyroid cancer (PTC) is an uncommon pediatric disease with an excellent prognosis. In follow-up surveillance, neck ultrasound (US), basal and thyroid-stimulating hormone-stimulated serum thyroglobulin (Tg) levels, and diagnostic whole-body radioactive iodine scans (DxWBS) have been traditionally used in both adults and children for the detection of recurrence or metastases of PTC. METHODS: Two pediatric patients with metastatic PTC were followed after standard ablative treatment with routine neck US and serum Tg levels, as well as periodic DxWBS. RESULTS: Neck US identified recurrent and metastatic PTC which DxWBS failed to detect. CONCLUSION: Neck US was superior to DxWBS in the detection of recurrent PTC in these 2 pediatric patients. These findings are consistent with the 2015 American Thyroid Association (ATA) Guidelines that neck US is an ideal imaging modality in pediatric patients for the surveillance of PTC local recurrence or lymph node metastases.

Clinical Implementation of Pharmacogenomics for Personalized Precision Medicine: Barriers and Solutions.

Clinical implementation of pharmacogenomics (PGx) leads to personalized medicine, which improves the efficacy, safety, and cost-effectiveness of treatments. Although PGx-based research has been conducted for more than a decade, several barriers have slowed down its widespread implementation in clinical practice. Globally, there is an imbalance in programs and solutions required to empower the clinical implementation of PGx between countries. Therefore, we aimed to review these issues comprehensively, determine the major barriers, and find the best solutions. Through an extensive review of ongoing clinical implementation programs, scientific, educational, ethical, legal, and social issues, information technology, and reimbursement were identified as the key barriers. The pace of global implementation of genomic medicine coincided with the resource limitations of each country. The key solutions identified for the earlier mentioned barriers are as follows: building of secure and suitable information technology infrastructure with integrated clinical decision support systems along with increasing PGx evidence, more regulations, reimbursement strategies for stakeholder's acceptance, incorporation of PGx education in all institutions and clinics, and PGx promotion to all health care professionals and patients. In conclusion, this review will be helpful for the better understanding of common barriers and solutions pertaining to the clinical application of PGx.

Biology and Conservation of the Taiwanese Humpback Dolphin, Sousa chinensis taiwanensis.

The humpback dolphins of the eastern Taiwan Strait were first discovered scientifically in 2002 and since then have received much research attention. We reviewed all information published in peer-reviewed scientific journals on these dolphins and where appropriate and available, peer-reviewed scientific workshop reports and graduate theses were also examined. Recent evidence demonstrated that this population warranted recognition as a subspecies, Sousa chinensis taiwanensis. It is found in a highly restricted and linear strip of coastal waters along central western Taiwan. Numbering fewer than 80 individuals and declining, five main threats (fisheries interactions, habitat loss and degradation, loss of freshwater to estuaries within their habitat, air and water pollution, and noise) threaten the future existence of this subspecies. These dolphins have cultural and religious importance and boast the highest level of legal protection for wildlife in Taiwan. However, despite enormous efforts by local and international non-governmental groups urging immediate conservation actions, there have been no real government efforts to mitigate any existing threats; instead, some of these threats have worsened. Based on recent studies, we suggest the IUCN Red List status be revised to Critically Endangered CR 2a(ii); D for the subspecies.

SHOX gene variants: growth hormone/insulin-like growth factor-1 status and response to growth hormone treatment.

CONTEXT: Short stature homeobox-containing gene (SHOX) variants of unknown clinical significance occur frequently among children with short stature, yet their growth hormone (GH)/insulin-like growth factor-1 (IGF-1) status and response to GH have not been studied. OBJECTIVE: To define GH and IGF-1 status in children with SHOX variants and assess their response to GH. PATIENTS AND METHODS: This is a retrospective review of children with short stature. Children with SHOX variants were compared to those with no variants. Height standard deviation scores (SDS) and IGF-1 SDS at baseline and during GH treatment at 6, 12, and 24 months were analyzed. Growth velocity (GV), maximum GH dose, IGF-BP3, and changes in height SDS, IGF-1 SDS, and GV were compared. RESULTS: Among 355 children, 83 (23%) had SHOX variants. Nineteen different SHOX variants were detected. There was no difference in age, height SDS, IGF-1 SDS, or IGF-BP3 between children with SHOX variants and those with normal SHOX. Height SDS, IGF-1 SDS, IGF-BP3, GV, and GH dose were not different between patients with SHOX variants and those without. CONCLUSIONS: The GH and IGF-1 characteristics of children with short stature were not different between children with SHOX+ variants and children with no variants. Although these findings suggest that SHOX variants are polymorphisms, studies prospectively comparing individual SHOX variants are needed.

Alanine transferase: An independent indicator of adiposity related comorbidity risk in youth.

BACKGROUND: Elevated levels of alanine aminotransferase (ALT) are associated with obesity and are often a consequence of non-alcoholic fatty liver disease (NAFLD). The aim of the present study was to assess the relationship between ALT and risk factors for adiposity-related co-morbidities in a diverse population of middle school children. METHODS: We measured height, weight, body fatness (bioelectrical impedance), waist circumference, insulin sensitivity, phase 1 insulin release (acute insulin response following intravenous glucose), beta-cell function (acute insulin response corrected for insulin sensitivity), ALT, lipid profiles, and circulating concentrations of interleukin-6 (IL-6), C-reactive protein, adiponectin, and tumor necrosis factor-α (TNF-α) in a multi-ethnic/racial population of 106 middle school students (aged 11-14 years, 45 female) of varying body mass indexes (BMI). RESULTS: Alanine aminotransferase was significantly correlated with BMI, % body fat, fat mass, waist circumference, fasting insulin, insulin resistance, triglycerides, and was inversely correlated with high-density lipoprotein cholesterol in children, even though all values of ALT were "normal" (range of 4.0-33.0 U/L). ALT was significantly higher in males than females even when corrected for body fatness. Significant correlations with lipids and insulin resistance persisted even when adjusted for age, gender, and body fatness. CONCLUSION: Even within the normative range, ALT levels were significantly correlated with anthropomorphic and biochemical risk factors for adiposity-related co-morbidities in youth. Therefore, because ALT is correlated with dyslipidemia, insulin resistance, and central fat distribution, it might also serve as a marker of risk for adiposity-related co-morbidities beyond NAFLD.

Magnetic resonance imaging as an adjunct to ultrasound in evaluating cesarean scar ectopic pregnancy.

Cesarean scar pregnancies (CSPs) are a relatively rare form of ectopic pregnancy in which the embryo is implanted within the fibrous scar of a previous cesarean section. A greater number of cases of CSPs are currently being reported as the rates of cesarean section are increasing globally and as detection of scar pregnancy has improved with use of transvaginal ultrasound (TVUS) with color Doppler imaging. Delayed diagnosis and management of this potentially life-threatening condition may result in complications, predominantly uterine rupture and hemorrhage with significant potential maternal morbidity. Diagnosis of a cesarean scar pregnancy (CSP) requires a high index of clinical suspicion, as up to 40% of patients may be asymptomatic. TVUS has a reported sensitivity of 84.6% and has become the imaging examination of choice for diagnosis of a CSP. Magnetic resonance imaging (MRI) has been used in a small number of patients as an adjunct to TVUS. In the present report, MRI is highlighted as a problem-solving tool capable of more precisely identifying the relationship of a CSP to adjacent structures, thereby providing additional information critical to directing appropriate patient management and therapy.

Racial/ethnic differences in clinical and biochemical type 2 diabetes mellitus risk factors in children.

OBJECTIVE: To examine whether periadolescent children demonstrate the significant racial/ethnic differences in body fatness relative to BMI and in the prevalence and relationship of body composition to risk factors for type 2 diabetes (T2DM) as in adults. DESIGN AND METHODS: Family history of obesity and T2DM, anthropometry, insulin sensitivity and secretory capacity, lipids, and cytokines (IL-6, CRP, TNF-α, and adiponectin) were examined in a cohort of 994 middle school students (47% male, 53%, female; 12% African American, 14% East Asian, 13% South Asian, 9% Caucasian, 44% Hispanic, and 8% other). RESULTS: Fractional body fat content was significantly greater at any BMI among South Asians. There were racial/ethnic specific differences in lipid profiles, insulin secretory capacity, insulin sensitivity, and inflammatory markers corrected for body fatness that are similar to those seen in adults. Family history of T2DM was associated with lower insulin secretory capacity while family history of obesity was more associated with insulin resistance. CONCLUSIONS: Children show some of the same racial/ethnic differences in risk factors for adiposity-related comorbidities as adults. BMI and waist circumference cutoffs to identify children at-risk for adiposity-related comorbidities should be adjusted by racial/ethnic group as well as other variables such as birthweight and family history.

CT of the skin and subcutaneous tissues.

A broad spectrum of skin and subcutaneous (SQ) findings may be discovered in the emergency setting on CT examinations. There are some findings that are directly relevant to the reason or reasons why the patient has undergone the CT examination. However, other findings may be incidental. The skin and SQ tissues are by definition on the periphery of CT images and may be overlooked by the radiologist, although findings related to them can be of clinical importance. The purpose of this pictorial essay is to present a broad spectrum of skin and subcutaneous findings which may be identified on CT examinations in the emergency setting (and in some cases nonemergently), and to briefly review the relevant imaging literature, which surprisingly is relatively limited on this topic. Categories of cutaneous and subcutaneous abnormalities that will be covered include trauma and hemorrhage, iatrogenic findings, infection, neoplasms, calcification, and other miscellaneous entities, all of which may initially present on emergency CT examinations of the body.